True. Apparently, Pickup+ resets the follower level to zero, and when the follower is placed, the stats are “re-rolled”/change.
I confirmed that Pickup+ was NOT responsible for the two issues I mentioned above. #2 is caused by Litman’s 100% female mod. My guess is that similar mods also produce this bug. I am still trying to figure out what is causing #1. If anyone figures this out please see my other post here