I propose that GnuPG stop shipping the .skel files (dirmngr.conf and gpg.conf), and stop installing them.
Ideally, GnuPG should work fine for the simple case with nothing in these configuration files in the user's GnuPG homedir.
Indeed, the currently-shipped gpg-conf.skel and dirmngr-conf.skel files are all empty -- all the text in them is commented out. So they're currently basically documentation.
If those files are copied into ~/.gnupg/ the first time the user runs gpg, then they simply get out of date once gpg is upgraded (because the new versions aren't copied over). If they're documentation, they should ship *as* documentation, not as conf files that are likely to become stale once installed by the user.