RE: Multi-colour printing
Let's get back to brass tacks here, OP wasn't looking for specifics on modifying his STLs here, as far as I'm able to tell?
We don't know if you can "hot change" (i.e. change while printing) filaments. While a head is not currently in use, it's just sitting in the cradle, each with their own feed tube. That's about all that is known at this point.
The easy solution for OP though, is just get enough heads (4 it seems?) to handle their printing without changing. If that's not viable due to cost, then, OP will have to wait for Prusa to officially say one way or the other -- everything else is speculation.
RE: Multi-colour printing
You only have to be there for a single color change, though. If you don't want to do that, order an XL with 3 heads instead of 2.
That’s the correct answer. If you need 3 colors and that’s your business, then that capex is what is needed to most efficiently generate parts. Tring to work around the right answer will likely yield a sub-optimal result if you want unattended operation. For me multimaterial and soluables is going to be a game changer