Hmm, now that you mention it yeah, that's a good point.

But in most situations I can think of, like choosing a feat you don't meet the prerequisite level or skill training for, it gives you a warning that you're doing something wrong. And if you want to overwrite the ability scores entirely you have to select an option that makes it explicit what you're doing.

This element seems different in that if—like I suspect my players might be—you're building directly in Pathbuilder without reference to the book or AoN, you could accidentally end up with an illegal character without realising it.

Thankfully with GM mode I can go in and check for them. And I didn't find this particular error in doing so (though did find one player who just never picked a skill increase at one level, one player who had accidentally picked up the same spell from both a heritage and a feat, and one who picked a feat pre-remaster that was given to the class for free post-remaster, so I'm glad I spent the time going over things). And it does enforce restrictions against something that no official option could have taken. No wizard can pick anything other than Intelligence as their class skill RAW, and Pathbuilder gives you no option here.

So I doubt this is a deliberate design choice, but probably either something that was overlooked, or even more likely a limitation of the way it's been coded which makes it impossible/more difficult than they think it's worth to enforce the restriction.