Note: This goes long as it addresses many issues with the amazing tools of manufacture that the question only raises tacitly.
Reading the tools one way…
There are a couple of different ways of reading the description of the amazing tools of manufacture. Here's the most restrictive:
In the hands of a casual wielder, these items simply appear to be magically enhanced masterwork tools for a specific Craft skill (determined randomly)[, but] in the hands of a craftsman with 6 or more ranks in the [previously] selected [at random by the GM] Craft skill,… [t]he wielder may use the tools to create items using the [previously determined] Craft skill much more surely and quickly. The wielder may take raw materials with a value equal to half the price of an object to be crafted, and produce a finished object in as little as 1 hour for an item with a final cost of 2,000 gp or less.
Using this reading, a creature that possesses 6 ranks in the skill Craft (alchemy) and that's using, essentially, amazing tools of alchemy manufacture can purchase raw materials and use the tools to produce from those raw materials any number of alchemical items each day as long as the market price of any individual item doesn't exceed 2,000 gp.
While this is extraordinarily strict for a 12,000 gp magic item that also increases how much a craftsman must typically spend on raw materials, using the Craft skill in a totally mundane fashion—that is, as printed—normally takes an excessively amount of time, and being able to manufacture quickly alchemical items in particular in such a fashion can be a significant boon to the right craftsman, especially if she's also an adventurer. However, under this strict reading, if the GM randomly determines that what's found or discovered is, instead, amazing tools of calligraphy manufacture or amazing tools of shoe manufacture, it will take an enterprising or ingenious adventurer to get much use from them, and such tools, despite claiming to be amazing, will likely end up as vendor trash.
…And reading the tools another way
An alternative and less strict reading eliminates [previously determined] from the above description, like this:
[I]n the hands of a craftsman with 6 or more ranks in the [previously] selected [at random by the GM] Craft skill,… [t]he wielder may use the tools to create items using the Craft skill much more surely and quickly. The wielder may take raw materials with a value equal to half the price of an object to be crafted, and produce a finished object in as little as 1 hour for an item with a final cost of 2,000 gp or less.
In this case, the Craft skill is instead read to mean any Craft skill. Thus, using this reading, a creature that possesses 6 ranks in the skill Craft (alchemy) and that's using, essentially, amazing tools of alchemy manufacture can purchase raw materials and use the tools to produce from those raw materials any number of mundane items of any kind each day as long as the market price of any individual item doesn't exceed 2,000 gp.
This means that, essentially, now and forevermore while the party is in possession of the tools the party no longer worries about carrying mundane supplies that cost individually up to 2,000 gp. An hour's labor by a creature whose 6 or more ranks in the skill Craft matches that of the tools can yield literally anything depending both on how many different Craft skill checks the creature can succeed on (as any item made using the tools still requires a Craft skill check be made for the item even if it's only ever one check per item) and how ubiquitous the GM views raw materials. (See this 3.5 answer for more information on the vagueness of raw materials; so far as I'm aware, the same (non)rules apply to Pathfinder.)
About the price of the tools
Either reading allows a user to employ the tools as a restricted but nonetheless use activated version of the spell fabricate, widely considered one of the game's most controversial spells because of its ability to ruin economies. According to Table: Estimating Magic Item Gold Piece Values (see here), a use-activated magic item of fabricate has a market price of 45,000 gp (5 for a 5th-level spell × 9 for a minimum caster level 9 ×2,000 for use activated ÷2 for the fabricate spell's instantaneous duration)… if the GM were to allow such an item into her campaign and didn't otherwise adjust the price.
Using either reading, it's possible that the author of the tools looked at their vast number of limitations and said, "Y'know, that combination of limitations looks like it should reduce the price of a use activated fabricate magic item by about 75%."
Likely which reading the reader prefers depends on whether the reader believes that that deep of a discount can only be justified by the more restrictive first reading or that such a discount remains valid even with that less restrictive second reading.
"What's the better reading?"
Honestly, the better reading is whatever's best for the campaign.
Both readings are interesting—the second more than the first—from a noncombat perspective. (Most folks will struggle to craft anything—even with the tools—during combat!) Under the first reading, the ability to make ridiculously expensive shoes in a hour probably holds little appeal to adventurers, but that's certainly a valid option for a non-adventurer, and that makes the tools into a plot device, something for adventurers to recover and return to their owner rather than to use themselves.
Under the second reading, the much more versatile but still limited tools are a luxury that allows adventurers to create from raw materials relatively inexpensive mundane items at will with a little effort. It's unlikely, as written, to break games like a use activated fabricate item would.
If the GM wants an interesting plot device, use the first reading. If the GM wants adventurers not to worry anymore about relatively inexpensive mundane items, use the second reading.
"Can the tools be used in conjunction with the feat Master Craftsman to create magic items?"
This GM would allow it. Probably someone can find a technicality that prevents the tools being used in conjunction with the feat Master Craftsman, what with the description of the tools saying, "The wielder may use the tools to create items using the Craft skill much more surely and quickly" (emphasis mine), and the feat Master Craftsman saying, "You must use the chosen skill for the check to create the item" (emphasis mine), but—damn!—that hair is simply too fine for even this part-time rules lawyer to split.
And, anyway, I wouldn't want to. The feat Master Craftsman is already so absurdly limited that I'm tempted to call it a trap. The feat gobbles valuable skill ranks. The feat eats at least 1 more feat by mandating the craftsman also possess either Craft Magic Arms and Armor or Craft Wondrous Item to do anything with it. It further limits the craftsman to creating only those magic items the GM allows her to make with that one Craft skill she picked when she took the feat. And she still just can't create spell-trigger or spell-activation item even if such an item does fall within the purview of her feats and skill. It's like the feat Master Craftsman has a grudge against players trying to use it.
So, sure, this GM would allow the user of the amazing tools to create with it magic items if she also invested all those resources into making the feat Master Craftsman go. If she produces magical weaponry or whatever at twice the normal rate—1,000 gp per day is typical, but the tools double this to 2,000 gp per day—, I can't imagine this being a problem.
"How does a creator that's using the tools create mithral full plate?"
Mithral full plate has a market price of 10,500 gp. (Just to be clear, as it's not a magic item, mithral full plate doesn't require the creator to possess the feat Craft Magic Arms and Armor therefore also doesn't require the feat Master Crasftsman.) The description of the amazing tools of manufacture, in part, says
For objects with a final cost of more than 2,000 gp, the wielder can perform 2,000 gp worth of work in a single hour, but only once each day. Only a single skill check is required to successfully complete the item, made on the last day of crafting and gaining the +4 circumstance bonus granted by the tools.
(Emphasis mine.) That final cost I can only assume is supposed to be market price. Hence the creator purchases 5,250 gp of raw materials and labors using the tools over the mithral full plate raw materials for 1 hour each day for 6 days. She completes 2,000 gp of work toward the mithral full plate on the first 5 days and 500 gp of work on day 6.
However, at the moment of completion on day 6 the creator makes a Craft (armor) skill check (DC 23; i.e. 10 base +9 for the armor bonus of full plate +4 for working with mithral). Normally, if a Craft check is failed by 4 or less, the craftsman makes no progress, and if it's failed by 5 or more, the craftsman "ruins half the raw materials and [must] pay half the original raw material cost again." Presumably, then, if a creator that's using the tools fails the one Craft skill check necessary to complete the item by less than 4, she can try again tomorrow, and she can even try again tomorrow if she fails by 5 or more, but to do that she'll also have to chip in 2,625 gp for the raw materials she somehow wasted.