[Ben Jenssen]

Yet another case where my preferred session setup will work just fine.
I, like many, have for years now set up our tracks to go to a aux track instead of the main outs that PT seems to default to. I call it MIX. It allows me to route the mix anywhere to monitor, print etc. Remember, PT let's you set a track's output to more than one destination. I put master plugins on MIX instead of a master fader, we all know that those are after fader, right. So I never have anything on MF. It's just a volume control.
But in your case, if you worked like this you would put the room EQ plugin on the MF and bounce or print the MIX aux.
I really like the flexibility of working this way. For example, I have outputs 1-2 going to my monitors, and 3-4 going to headphones. I switch the output of MIX to 3-4, and I have it on headphones, and the monitors are silent. Very handy.