What's wrong with having DataStore as a require dependency & let the packager / clients work accordingly? The only real problem is the standalone ZIP doesn't include the required dependency, a simple note on the description page should handle that nicely.
Using the Required Dependency IMO is the better of solutions here than trying to redesign the curseforge system.
You covered it all. Either you break the client or standalone users have to download two addons to make it work. Personally I think it might be a little easier on the users if the stub addon was marked in .pkgmeta as a required dependency but only as an optional dependency in the toc so that the addon would still load but could popup a clean message box informing the user that the stub addon is missing and where they can download it. Also marking the stub as LoD would let the main addons enable it and load it even if it was disabled instead of telling the user to download it when they already have it.
Well the problem of the client identifying the wrong addon because multiple addons include the same directory with the same content still exists if multiple addons are just including a directory with nothing but a .toc listing a saved var. It is a serious issue that has been around since updater clients have existed.
To make it perfectly clear what I'm talking about I'll give a real example of a past situation. There was some guide addon similar to TourGuide or some of the paid leveling guides (but it was rather bad so nobody really remembers the name of it) that was using TomTom for the direction arrow. The addon included the top level TomTom directory in its zip file and sundenly a lot of users were reporting that some crappy guide addon got installed somehow by the client but they never installed it and didnt want it. Whenever they deleted the directory the client would just reinstall it. It was discovered that the client was seeing the TomTom directory and thought it was part of the guide addon so it should update that guide addon instead of seeing it as the TomTom addon. The solution was to purge all records of the zip files from the database and physically delete the files from the server. That was a very drastic solution when you consider that Curse never deletes anything, when you mark a file as deleted it still exists but its just hidden from normal users, only the project owner and the admins can see it.