Let's just call them build checks and be done with it. They make sense from a game perspective, but the 3E/3.5E point buy rules make them useless as stat checks.
Let's say I have a puzzle. I want an intelligent character to be able to figure out this puzzle in-game without the the player needing to resort to player knowledge instead of character knowledge. Also, I don't want a level 1 wizard to be able to do it. Even lowly hedge wizards are going to have 14/15 intelligence; however a sorcerer never will. Other than wizard, only a rogue has a realistic chance as they may have put some points into intelligence to get more skills. So you either have to make the check so low anyone can succeed, or so high only specific classes/builds can. Has anyone in history ever made a 15 intelligence fighter, or paladin?
Did you know adult dragons start at 23 strength (adult black and brass)? That's right, your fighter is stronger than an adult dragon! That should be impossible.
Similarly, why are 1st level neophyte clerics wiser than grizzled epic rogues who have 20+ levels of experience to draw on? Maybe classes should get a wisdom bonus as they advance in levels.
Anyway I do see a way around it. Limit character abilities to an unmodified 16 to 18 pre-epic. That way people would throw some points into alternate stats. Then we'd occasionally see a smart paladin.