Seems that the topic have been pretty active recently 
Just for you all to know everything is running smoothly since I’ve been asking for help. I’ve never had any problem so far for my usage and in my setting which is a bit specific:
- The git repo is not very active (< 2 commits / push / pull a day)
- I’m the only user of the repo
- Syncthing is NOT always running in the background; for conservative reasons, I only fire it up when I have to sync my computers before heading out or after getting back
Generally speaking I’d advise not to push/pull/commit git repos while having Syncthing running in order to lower the synchronizations required. I’ve got no objective reason to do so but it seems just more logical and clean.
My 2 cents.