I do something like this, under Linux and Windows. I have @file nodes with names like this:
@file .{{sep}}docs{{sep}}myfilename.mwiki
(this is a 'mediawiki' file).
The {{sep}} gets magically converted to '\' under Windows and '/' under Linux. I think there are other keywords available with this {{...}}syntax; look for a thread "cross-platform file references - how to deal with?"
As shown this keeps the @file within the main Leo file directory, under a 'docs' subdirectory in this case; I use it with Owncloud in a similar way to your use of Sync. I presume that with the sue of symbolic links, under Linux at least one could put them somewhere else. However I haven't yet pursued this.
HTH
Jon N