personally, everyone has there own prefered ways. I am one who likes to jamb parts and install prior to avoid handling and risking damage to fresh paint work, concentrate just on painting the exterior, and plus I have limited space at home. Unless it is a special paint job that must be sprayed very consistantly for match like a candy, I see no problems jambing parts first, installing and then painting. But you must make sure any parts are protected from overspray. Jambs and underhood areas can be masked in a way where there is little or no line if you can choose a good place to mask, backmasking and you open and check how the areas are looking color has got in as far as any sealer if used, and covered good with clear, and shoot a blending solvent or reducer on the edge if you feel its needed. If painted with everything torn apart, it may mean less masking, no lines and possibly make it easier to get a clean job, as long as panels are sitting right and done under the same conditions, and care is taken in reinstallation. If they do the job properly, and necessary precautions are taken, either really should work fine IMO, people find the ways they like doing things, and what works for them.
And the primer, its not really it continues to flow, it continues to shrink and takes time for solvents to completely evaporate. Shouldn't be a huge issue if good 2k products are used, bodywork is finished well, and good flash times and the coats of primer are not piled on. Abuse primer and it can mean problems showing up down the road, such as dieback or sandscratches showing, even though everything looked fine when painted. I believe it is shine that said he only uses epoxy now cause of issues he has with other primer types.