Thanks for clarification and contribution @ceri_waters - always a pleasure. I think I will leave the discussion here, but ofcourse open.
Might be an anti climax for the thread, but I’ve actually - post getting it to work - decided not even to implement it. Honestly I think it became too sketchy and too over engineered, for what I use it for. It’s very rare I actually work with expansion stores, so simply having a README/mental flow pulling theme changes before working and simply CLI pushing sequentially, is sufficient for my case.
I’ve become a huge single store advocate, using Markets and blended stores for B2B+B2C customers. Hooray for the Markets UI and APIs whenever it get launched.
For future readers; as the native integration works today, I think going with @ceri_waters workflow is the best solution.