I think I'm just going to ignore the versioning issue so far as trying to create default "ignore" files. Module::Starter has options to do this, but I think it is easier for the user to just create a local profile dir and add whatever files she thinks are needed. The standard M::C templates will be pulled in if they are not in the local dir (assuming the profile name exists in the standard distro) so it should be trivial to add one's favorite versioning config files or LICENSE or whatever without having to deal with every file in the standard distro profile.
M::C will then generate the MANIFEST file (via MakeMaker) once all files have been generated. And of course, one could have a custom MANIFEST.SKIP in the local profile dir, as well. I can easily see a normal use-case where the local default profile dir would only have a couple of files in it, with everything else coming from the standard distro default profile.
It helps to remember that the primary goal is to drain the swamp even when you are hip-deep in alligators.