Let's say that a player creates a 6th level character with maximum possible ranks in craft (armorsmithing) . They want to start with selfmade full plate armor. Should they still cover the full price of the armor or just the materials, which are one third of the price? I believe that selfmade starting gear should be less pricey than one bought on the market. On the other hand I am afraid, it could be heavily exploited, like starting with +5 adamantium battle plate armor. Are there any books, including third parties covering how to deal with this problem?
The rules expressly allow self-made starting magic items at higher levels.
Dungeon Master's Guide (3.5) p.199 gives the official rules for starting a new character above 1st level. The most relevant section is under Magic Items as Gear:
Character-Created Magic Items: A PC spellcaster created at a level higher than 1st can use any of the XP and gp you have awarded to make magic items, provided that she has the proper item creation feats and prerequisites.
However, advice on what items to allow are also given, with particular guidance on avoiding PCs spending all their starting wealth with one overpowered item.
You're free to limit what magic items characters can choose when they create characters of higher levels, just as if you were assigning those items to treasure hoards in the game. You can exercise an item-by-item veto, but an easier method is to use a maximum cost for a single item as a limit. [...] You could also limit characters to a certain type of magic item.
Character creation does not happen in the way that a 6th level character pops into existence with a huge bag of gold pieces and then goes to the ACME store and buy stuff. The price of an item at character creation represents the value. The fact that the character is able to create it just provides one way to explain why he has the item and it can also give good roleplaying opportunities. But I don't see why they should get it cheaper.
It's all in the past, and the money only represents the value, the origin is irrelevant.