I have been thinking about how flexible this really is, but while it lifts all kinds of technical restrictions, there still will remain some logical restrictions.
For example, the tech tree needs to be coordinated, layout and dependency wise. You cannot remove or add a tech without adjusting the tech after it (to tell it it now has a different predecessor), of course if you remove a tech, all units which require it need to be adjusted as well etc. So even with WoC there needs to be some coordination when merging mods.
To make the integration easier, there probably should be some conventions established (where to put files, what to call them, how to structure files (i.e. what part of a definition goes there), are you working on anything in that direction ?