I was using the metal prep on a block and cylinder heads. It converted the rust to a good clean surface and I never had a problem with the coatings on that engine. It got black, silver, and the bare aluminum coatings. I went the extra yard on prep on that one because I wasn't going to remove that motor ever again.
I've also never had problems when using on surfaces that were properly scraped and sanded. So I don't know if the prep is 100% necessary, but in the case of that engine, I didn't want some nook or crannie starting to rust again and lifting the coating because it wasn't sanded and prepped properly. Some items done without metal prep (radiator support, power steering box, a-arms, frame). All came out ok for me. I guess it'* a matter of how much you want to do.
I've topcoated according to the directions...no problems. But you want to make sure you do it within the curing time as directed. I never tried topcoating after a full cure, with the additional sanding an all.
I've never had a failure of POR-15 yet. I always followed directions (except for the gloves the first time) and always got good results. I believe taking time on the prep (degreasing properly, wire brushing, sanding, scraping) all are the key to allowing the product to do it'* job properly. Give it a proper surface and it'll work.