Yes there can be some conflicts. Some plugins specifically allow a way to differentiate settings per OS, but many do not. I know there are possibly different solutions out there, but I use this viewtopic.php?f=6&t=5840#p25515. Essentially it lets me target certain files I want to be OS specific, and I can back them up to OS specific folders. I sync the OS agnostic settings and the backed up OS specific files (not the original OS specific files). I won't go into all the details here, but the link I provided points you to a thread that can direct you to the plugin and a little more info on how I use it. Since it points the the settings file in my actual git User repo, you can look around and see how I set it up. I would look at the ST3 branch. I don't really use the ST2 main branch anymore. And like I said there are other solutions out there, so you don't have to take my suggestion, it is just what works for me.