I think we all assumed you were wanting to run the Challenge Series and now seeing that you are running SCCA in ITE, I would suggest printing off the supplements from the Viper Racing League.
I do know that many of the guys, years ago , that ran the RT10s , did take out the window, and it makes sense since it is removable like the side windows.
I would suggest you request Scott to send you a note on Viper Days Racing League Letterhead simply stating that a revision is being made to the Viper Days rules to make the rear window removable, since it is not a fixed unit, just like the side windows and could be a safety hazard. I would imagine this issue was overlooked as there are few RT10s running in the Viper Racing League anymore.
Good luck, but likely not much of an issue, and you should be fine with the roof on according to the VRL rules. I can't say I ever remember seeing an RT10 race without a roof.