Today I played a bit more and found a couple more bugs/issues with controller mode.
1) UI freezing while sorting still happens! (though seems less frequent)
It seems to happen slightly later than before because the sort UI overlay goes away before it freezes whereas before it froze before that UI vanished 100% of the time.
2) Take all items no longer closes the open container.
On PC when hitting Y to take all items from a container you are left with an open container and must manually close it. Previously take all items would close the container.
