It's a good question and it got me thinking. My plan is to finish for M:C and then make a modcomp for BTS, but if more versions are still in use, then what?
Thinking about a proper answer to this question made me realize something really important. Right now the editor is hardcoded to read the path of the DLL and then use that one for reading and writing files. What if it is possible to add an XML file, which tells the path of the mod? This would allow making an editor mod, which can be used on all mods even without modifying the code in those mods. If exe paths are set as well in that new XML file, then editor and mod will not even have to use the same exe file.
The result from this approach is that I can make a standalone editor as a colonization mod and it can be used by everybody regardless of which version of civ4 they mod. It shouldn't be hard to make an editor mod for BTS as well, but using the Colonization version is highly recommended because only the Colonization exe supports drag-n-drop and the editor use that. This means the BTS version will be a worse editor and there is nothing I can do about that.
The only issue I can see with editing a "remote" mod is the button preview. However this can be solved by just copying the Art folder. Most likely a symbolic link will be a better solution, though it takes more skill to set up. Either approach should work.
This requires some thinking and some testing, but I think I'm on to something really interesting here. Making this standalone setup will not prevent mods from including the editor in their own source code. This is just added flexibility.