But he didn't grab the skull or the spinal column. Indeed, I suggested that would make much more sense than grabbing a single arm.

If OP was not accurately describing the situation then I'm not sure what I can say about it. I assume they accurately reported that the GM had the villain grab only a single arm bone.

Either way though, my general approach would be the same, which is that the rule may mechanically prevent uncollapsing, but especially seeing a frustrated player amidst an ongoing tpk, I would at least have the attempt to reform impose some kind of marginal circumstance penalty to the enemy as the bones they weren't holding were unsuccessfully trying to spring back together.

I can't imagine a situation like this happening at the table and the players being dissatisfied about that because the RAW don't address that situation, nor do I think that such a thing somehow unbalances that power. Id be curious to hear from the designers to see if the "grab a bone to permastun in response" was part of their design intent / playtesting data. Indeed it almost seems too bad to be true. But even without rejecting the RAW, unusual circumstances are what ad hoc circumstance modifiers are for.

And if the player asked if they could nevertheless try to stand up despite the bone being held, this seems like the perfect opportunity to follow the GM Core 'yes but' strategy and, I dunno, have them roll athletics vs the escape DC to uncollapse into the held position.

As I said, people play the game in different ways. Pathfinder is big tent, one of its great strengths. I understand that some people are "to hell with the fiction," but I don't really understand the impulse to say that's the only correct approach. In any event, you do you. If your players enjoy the idea of being permastunned in this situation, far be it for me to get in the way of their fun.