Well, this is a regression due to us creating creating /run/user/gnupg/ socket directories now on the fly. Thus there is no more need to create non-default home directories via gpgconf. Now, gpg-agent watches the socket file and terminates itself as soon as the socket file vanishes. Before that change the socket for a non-default home directory was created in the homedir itself and thus removing the homedir also removed the socket file and in turn gpg-agent terminated itself.

The solution is to also watch the home directory...