Ok, so I tried today to fix the issue that one cannot use buttons & doors on other user’s lots. When I did that, suddenly everyone could access all chests. When I tried to fix that, everyone was able to break blocks everywhere.
So the current version of WorldGuard has some bugs that we have to live with. Otherwise I have to do an extremely messy downgrade to the last version which would roll back lot changes (i.e. new users etc) since the upgrade.
I managed now to fix it by assigning region flags for allowing buttons use and denying chest access for all 6700 lots individually. I was hoping to fix that with 1 flag per world, but there are currently bugs in the system that prevent that.