The idea I always like to float by people who go for a 3 PU guitar is to consider a HS P90 middle PU. Fat like HB still, but with the full frequency response of a SC. Distincly nice midrange roar and amazing definition. Combines in cool ways with the HBs too. It then kinda is like a supercharged take on a HSH guitar. For prog projects I can very much see that added versatility and the P90 sound working. Add some nice wiring options and you got yourself something special that can do a heck of a lot of things.
Going with a C-bomb set my choice would probably be a MQ, giving a bit of a vintage variety kick in between, but being able to (I think) keep up in output and all. Similar idea as the RY is. You could also do a Stockholm or Supermassive (rather the later, but that would have to be a custom, which they normally do though).
Now I know this is not for everyone and most people like to dismiss P90s of the bat, but I recommend you at least look into it.