I explicitly dislike the idea of using Git as the backing store. Forget the fact that Git is not native on Windows and is immensely bloated; the actual .git folder is a mess for backup systems when working locally compared to a single database file.
Sure but there is a big difference between being stored once (modulo backups) on a central server, and every developer needing to download all the resources for every issue and the entire wiki in order to work on the code at all. It works fine for sqlite, because they only have a handful of developers, so it's not a big deal for them each to have their own local copy of everything. But having to download GBs of issue and wiki data in order to make a pull request (however that would work with fossil) or otherwise contribute is a significant barrier to entry.