I am not a professional at anything but...
When I do bodywork I don't worry about the rubber seals until the last thing for three reasons. One, if your using primer as a build up when your blocking there is gonna be overspray all over the rubber even if you mask it. Two, you still have to paint the jams color so you wouldn't do that until all the priming was done and three, the metal hinges and door strikers will overcome any seals that didn't seat correctly.
It's a good Idea to install the little square rubber bumpers on the doors and trunk lid temporarily for lining up and blocking but then remove them for final paint and reinstall them along with the seals as the very last thing