I have removed my original thin metal chromed HiPo style valve covers several times over the past 44 years with the motor in the car. It takes a lot of patience, but you can snake them out. The back bolts are a real pain to get in and out, especially in. I can see how allen head bolts could be a big help. My relevant experience ends there.
If you have roller rockers it is likely to be more of a problem since they require polylok type nuts on the studs and thus stick up higher, reducing clearance. I have heard that you can use them with the thin metal covers but have to take the baffles out. I will leave that for others to confirm. Using the thick cast aluminum Powered By Ford covers might be more of a problem, but I have no direct experience with that either, yet. Regards, Gene