could you disable the bind-dirs and see if it works? If so, enable bind-dirs one by one until it stop working
Commented out all user entries in bind-dirs config, did not help. Tried removing all snaps and reinstalling snapd, did not help either.
Try to create a new qube and move the files in /rw from the problematic qube. First all of them at once and if it won’t work then by parts.
That’s what I am going to do. But it happened to multiple qubes (and not quite identical templates), so I thought maybe it is a known problem.
Could you try to disable selinux in rc.local and see if the qube works better? setenforce 0 to disable selinux
maybe Selinux rules changed meanwhile and some attributes in your qube are not right anymore (or were changed manually). 
it would be nice to figure what causes the issue because I don’t think you will be alone with this problem
Tried already 
Just a wild guess: do you have qubes-core-agent-passwordless-root installed in f40 qubes? Would you try with that, if not installed already?
Yes it is (however, the root sudo access is confirmed via dom0 dialog)