The more research on this bug i do, the older and older the posts get. I have now seen posts on this bug from 10 years ago, which sound exactly the same, but it's back when "Flextime" was referred to as "Elastic Audio." Apple has made no official recommendation, or fix in any of the updates and it really seems to be that they cannot mitigate the problem. It also seems that no matter how powerful the mac it runs on is, the issue still happens and is still exactly the same. The audio continues, the play head freezes, and you cant do anything until you click ok in the notification.
My iMac specs are:
27" 2020 retina 5K
3.6 GHz 10-core i9
128 GM Ram............ and i still get it anytime i use flextime. So it's the inability of Logic Pro to correctly process it, rather than the machine itself as has been mentioned in some of these older posts.
It seems like one of the most common "fixes" is to use the bounce-in-place function to reduce the number of tracks using flex at one time. i have yet to try that approach as i have only tried the "shutting off flex for the problem child region" but that has proven to be unreliable.
Next time i get going on a new session, if it happens i'll try to bounce in-place and let the forum know how it worked out.
Another method i have on deck seems super undesirable, but it just may be workable. my plan would be to track everything in garage band using that simplified interface and then export the finished stems when the "performance" of them is completed and edited, then do all my mixing and plug in editing/mastering in logic. but that just seems like a PITA last resort type of thing. Sort of like buying a Tesla and putting a Hemi in it because the battery keeps dying immediately. haha. but i digress.
The other thing i may fool around with is taking that sample session that came with Logic Pro (i think it's "Colors" by Beck IIRC) and try to record a few more tracks into that session which is already pretty involved to see if i can create the error in there (that session does not have this error and it has a ton of tracks... there has to be a reason for that and it can't just be that none of them use flex.)
Just some thoughts.