Whey separation

No, it doesn't. I make yogurt in my Instant Pot about once a week or so. The point of straining it for Greek Yogurt is to remove extra whey, so spooning it off at the start means less time draining. As a rule, you only get significant whey separation if the yogurt sits for a while after maximum coagulation is achieved, and the solids sink and contract. In that case, you can get a tarter end product than you might have expected, and a little more whey.

I don't make yogurt in an instant pot - but since no one else seems to be answering I would say no.
To make greek yogurt from regular yogurt you strain it to remove the whey so stirring it back in seems counter productive. Good luck