Very much a gray area. Your question title seems to refer to the notion of “text-trumps-table,” which is a rule set forth in the errata files for 3.5, but in this case there is not an explicit contradiction between the text and the table: the table just puts in a restriction not mentioned in the text. On the other hand, nowhere that I can find do the rules explicitly tell you to reference the table on this point, which it should.
In the case of the artificer (Eberron Campaign Setting) and his Craft Homunculus feature, we have an easy case: the class feature’s text explicitly states a limit on the homunculus’s HD, which is the clear-cut rule for artificers using that class feature to create homunculi.
Unfortunately, the easy answer ends there. The Craft Construct feat doesn’t mention anything about HD; it just says you can make a construct and see the individual monster entries for costs and the like.
In the case of golems, we have this rule:
Note: The market price of an advanced golem (a golem with more Hit Dice than the typical golem described in each entry) is increased by 5,000 gp for each additional Hit Die, and increased by an additional 50,000 gp if the golem’s size increases. The XP cost for creating an advanced golem is equal to 1/25 the advanced golem’s market price minus the cost of the special materials required.
Which unfortunately does not explicitly address the limits in the Advancement section of the stat block (though it does reference the Advancement section when it talks about size increases, since size increases are also indicated by the Advancement block)
And for homunculi crafted using Craft Construct rather than Craft Homunuli, we have
A homunculus with more than 2 Hit Dice can be created, but each additional Hit Die adds +2,000 gp to the cost to create.
Again, no reference to a maximum, though the table has “Advancement: 3-6 HD (Tiny)”
The shield guardian has a similar rule:
A shield guardian with more than 15 Hit Dice can be created, but each additional Hit Die adds +5,000 gp to the market price, and the price increases by +20,000 gp if the creature’s size increases to Huge, modifying the cost to create accordingly.
Again, no maximum. And that covers all of the Constructs in the Monster Manual that can be created with Craft Construct. Animated objects require animate object, and retriever demons and inevitables cannot be crafted.
The errata for Monster Manual did not touch on this point, which leaves us without RAW. The only thing I can offer is this: mindless constructs, such as golems and the shield guardian, are unlikely to advance on their own. They lack the capacity for learning. So I think that really, what else can the Advancement maximums refer to if not the HD added by the creator? If we do not use those lines for this, they don’t seem likely to be used at all. Moreover, adding more HD to a Construct is already referencing the Advancement section when it talks about size changes: those have to come from the Advancement line. So for a Construct, Advancement means the creator adding more HD, and thus that limit applies.
The artificer’s Craft Homunulus feature overrides that limit, though, since it does explicitly provide a different limit.