So we had this bug for a while, and the solution was just using an other dir, so the user later can merge the contents of the two dirs.
Sigh, testing the setup still takes a lot of time. For example to test the above bug, you need to do a base install, which still takes a lot of time. Hopefully sooner or later we can switch to kvm (as the old kvm-incompatible hw gets unused) and then this can be faster.