i had the same problem.
my approach: storing project data in a directory managed by owncloud
The Project X is created at workstation A, with a custom path pointing to a new sub directory of my ownCloud hierarchy. The default workspace is still residenting on the file system of A.
When I'm sitting at workstation B I open the default local workspace (local on B) and create a new project using the existing sources in the "synchronized" ownCloud directory.
Just click refresh any time you fire up eclipse and you have the current project data. Synchronisation runs in the background automagically, so take care when you have finished working to close eclipse and give ownCloud a chance for uploading the new files to the ownCloud server.
Tomcat or other Servers are running local, the config is copied manually between the machines via scp. This happens only if there are changes in the server setup, which is not very often.
I had no compatibility problems using NEON 2 (arch linux) & NEON 3 (download an running on debian stretch) with different JDK's yet.
Best regards
Armin