I didn't go through the entire game, so its entirely possible that it would not affect this particular "design". But as its far more educational than practical, I think its still worth mentioning.
> Especially because the d-flipflops found in standard cell libraries are frequently implemented as what amounts to two muxes and some inverters.
I'm curious where you've seen that implementation because I've never seen anything like that. Most of what I've seen uses two tri-state inverter latches.