Are you doing a minimal install when you install the resulting system though? If not what I suspect is going on is that there is a /var/lib/dpkg/status file in the ubuntu-server-minimal.ubuntu-server.squashfs file that is masking the changes you are making to the status file in the lower layer. In general modifying the base layer and then overlaying it with a layer that was based on the unmodified base is going to be skating on the edge of reasonable behaviour...
Are you doing a minimal install when you install the resulting system though? If not what I suspect is going on is that there is a /var/lib/ dpkg/status file in the ubuntu- server- minimal. ubuntu- server. squashfs file that is masking the changes you are making to the status file in the lower layer. In general modifying the base layer and then overlaying it with a layer that was based on the unmodified base is going to be skating on the edge of reasonable behaviour...