I cannot help but wonder if this change was forced upon github by Microsoft because gzip is GPL 3, maybe this other version is a clean room clone. We all know corporations hate GPLv3, including the large corporation I work for.
Furthermore, gzip isn't even necessarily the best tool to produce gzip data. If you want multi-core parallelism there's pigz, and if you're willing to trade higher CPU usage to get a better compression ratio you can use zopfli. I don't know the details of the implementation in git and whether it tries to leverage multi-threading or zopfli-like techniques, but the point stands that gzip isn't the final word on producing gzip data.
As much as I distrust Microsoft, I don't think there were any ulterior motives here.