I have built an addition that includes adding new plumbing. I am about to submit my plumbing plan and proceed with the rough in. When I have my rough in inspection I will not have my finished floor in yet so I would be guessing at the height of the closet flange at this point in time. Can I just run my closet DWV pipe up above the subfloor for the inspection and install the closet flange later? If so, should I install some sort of cap on the pipe to avoid gases during this time?

Can I just run my closet DWV pipe up above the subfloor for the inspection and install the closet flange later? If so,
You don't have to have a flange installed for a rough inspection.

should I install some sort of cap on the pipe to avoid gases during this time?
You do know that you will be required to plug up ALL OPENINGS with test balls or test plugs, (see image) and go up on the roof, fill the lavatory vent stack with water and let it setr for 8 hours before inspection. Call your local Building Department to make sure.
Good luck on your inspection. Tom

Tom nailed it. I am enclosing photo of toilet stub out. Here, instead of plugs, plumber used PVC cap glued onto the pipe .