- No support for LFS
- No support for hooks (precommit, etc)
- No? Bad? support for submodules
- No? Bad? support for line ending styles
If you don't care about those, you _should_ be able to use jj completely "undetected". It does encourage rewriting history more than some git workflows like.
In terms of issues in the git repo -- there shouldn't be any. jj uses git as a backend, all commits are stored as git commits, etc. If you colocate the repo, you're able to use git commands directly.