That is a challenge that I am contemplating for my next project.
One thought is to mask off the glue line and then prime the whole tube. Once the whole thing is primed, it should be an easy matter to mask off the outside and paint the inside.
The other option would be to attach the tube fins, and prime the rocket as usual. Once everything is primed, carefully mask the inside edges of the tubes and apply liquid masking to the outside edges leaving enough to overlap with tape on the outside, then mask everything else off and spray the inside.
I have had some other thoughts on this but they are really just variations and combinations of the same techniques.