If you plan on putting a new top one you can paint under it how ever they will have to scuff the clear to glue the new top down.. At the shop I worked at we would either leave the roof in primer or spray base only if there was a top being installed.
BIG mistake! Primer and/or base is open pour and moisture will get through it. Clear it to seal it then they can scuff the clearcoat. Itsa choice you will have to make.
My personal opinion is to spend the cash and BC/CC. It will be the last paintjob you will ever need if done properly. Some folks on this site prefer Single stage finishes. Do your homework on different finishes/vendors. I use PPG products as well as ALSA products. Both are "Quality" products.
If you are a novice bodyman take your time and spend the cash for the right products. I NEVER use Bondo!!!! Roof to 1/4 seams will need to be addressed. I always take the time to weld these seams so cracks won't appear later. Fill with "Allmetal" filler to smooth the seams and use Evercoat green label final coat to finish. There are many threads in here that you can refer too for more info. as stated by previous poster. Good luck and take your time. Bodywork cannot be rushed. Remember, primer does "not" seal the substrate. It must have final coat to stop moisture from entering. There are some 2K sealers that work if used properly.