Use git versioning to prevent unwanted changes on multiple installations
If git is installed (and can be found in PATH or its path is stated in settings), use it to create a repo in sync folder, and then automatically commit/push and pull/merge (automatically if possible) the synced content. This should prevent problems with keeping different sets of settings on different machines and unwanted overrides.
Or just put the folder into the dropbox.... so not a big deal
I have my sublime settings put into OneDrive, and have encountered an issue when after new installation of Sublime on second (next) machine and automatic installing some packages after syncing by the plugin, some settings are changed and so propagated to the cloud as fresh changes causing stored changes to be overriden. Also I want to have some base settings in the cloud with some differences on machines. A versioning system may help, I think. I will try to implement this functionality by myself.
Just to make my idea more clear: I'm talking about a repo in the cloud, not local.
some solutions:
Built in versioning of cloud provider
Many of the cloud providers have an "History of File" functions, which already tracks changes of the files. Normally it's accessible through the web interface. I know Dropbox and copy.com have this functionality (gDrive called this activities?)
Use Sparkleshare
Sparkleshare does auto syncing of folders quite like Dropbox. But it uses a git repo as a storage provider. So it does what you want auto commit/push/pull of your settings to a git repo.
Use existing Sublime Text plugin: STsync
STsync is also a Sublime Text plugin, which also auto sync Sublime Text settings but with a github.com repo instead of another folder like this plugin here.