This is a reasonable option. Indeed, we strongly considered this (i still have some CM4 modules and CM4 development board) when conceiving the new main board, but we decided to use the “standard” Pi4 because the CM4 doesn’t have USB3 ports and only an USB-2 port, what complicates design quit a bit, specially if you want USB-3. Keeping a foot in the tinkering and DIY world was in our minds too, of course.
When CM5 is released, we will reconsider this question. Very probably, USB-3 will be integrated in the CM this time.
Regarding the development of a computing circuitry for zynthian, i don’t consider this in the near-medium term. It’s too complex and the required financial muscle is huge. And really, from a strictly zynthianic POV, i think there is little reward on it. In spain we just to say: “zapatero a tus zapatos” 
All the best,