When we isolate a clipping group, it’s like we are jumping in a whole in a canvas and start dealing with what’s behind it. Whatever we move while inside isolated, would be visible through the hole.

So when we say Select All while being isolated, we usually don’t mean 'Select the stuff behind the hole and the hole itself' — it’s about clipped content only. Otherwise why isolate in the first place?

Select contents only first and and the clipping mask to the selection only when Select All is called again, if the clipped content is fully selected already. Display a hint to guide users.