I don't know how the amp channels are triggered but from an overall perspective, yes, you can keep the same pedal order and you wouldn't need the buffer as the Musicomlab has one built in.
The constraints are
The Musicomlab is not an ABY pedal, so you'd need an amp switcher. The way around this would be to use the first loop for amp 1 and the second loop for amp 2. This would remove the possibility for effects in the amps loop.
The pedals in the loop would only be assignable to one amp.
If you're only using one amp in the rig at a time then it's all possible. Channel switching and effects in the loop. All switchable at the touch of a single button.
The constraints are
The Musicomlab is not an ABY pedal, so you'd need an amp switcher. The way around this would be to use the first loop for amp 1 and the second loop for amp 2. This would remove the possibility for effects in the amps loop.
The pedals in the loop would only be assignable to one amp.
If you're only using one amp in the rig at a time then it's all possible. Channel switching and effects in the loop. All switchable at the touch of a single button.