Wouldn't encrypted files with a service like Dropbox help? Containers usually sync well (only syncs changed parts). Only downside is that you can't access files without decryption software.
Dropbox, as all other "just-works" sync services, don't handle merge conflicts very good. Suddenly you have thousands of Filename_EditedByX(3).txt in every folder and dont know which one of them is the newest and don't have their most common ancestor version easily available for a 3-way merge.
To be fair, they cannot handle merge conflicts with encrypted containers. I find that merge conflicts almost always cause more trouble than the work of avoiding them from the start. As long as you don't share data (with containers unlikely), merge conflicts should be extremely rare (and anticipated).