Hi Scott,
long time no see.
I'd also prefer github issues, yet as Andrew stated looks like we got to wait a bit for that to be an option.
If that's really going to happen in a rather short time (i.e. locationtech enabling github issues and porting bugzilla issues to github's), I'd chose that path, since the JIRA option is not supported either yet. That'd be a choice thinking on the project rather than personal preference, cause I too find bugzilla cumbersome.
In any case, I've always advocated for not linking commit messages to github issues by including #<issue number>, but instead write comprehensive commit messages, exactly because of this kind of situations. Over the years we faced the same problems a couple times in geotools/geoserver and, though practical in principle, that proved to be a rather short sighted approach. I find it's much better to have concise commit messages that are complementary to the actual changes, so that you can look at the patch and the reasoning behind it at a single shot with a simple git log.
/rant
Gabriel