This happens to me too but is, I suspect, a problem/feature of Unity as it happens with non Spine files as well.
Meta files has always been a fiddly issue with git and subversion. Unfortunately at this time, your team should be submitting meta files for their own assets, once. And then everyone else should be discarding and being careful what they commit to prevent conflicts.
Fixing this in Spine would be great, but what about all the other files that Unity decided at random, that have "changed". Hell sometimes I can just look at a shader or material in shader and Unity decides it has "changed". If anyone has a solution to this, not just for Spine but for any file types with meta and git. I'd love to hear about it too. 🙂
PS In our teams we only have programmers handle git now. Designers and artists etc, they just commit theit stuff to somewhere on LAN. When assets such as Spine are needed, programmers put the assets in the project themselves. Leave the meta stuff to the coders only (Gulp 😉 )