I was cloning from yours clone on github (https://github.com/wikimedia/pywikibot-core).
If git should be wikimedia VCS of choice, head/master should be maintained in git.
I haven't tested it, but it seems reasonable, that every operation of svn2git crate new hashtags of commits in git and from point of view of git repository they aren't identical, so merging that repository make mess in history of commits.