My disclaimer: I am no expert on those vintage of trucks.
First of all you sound like a guy just like myself, I prefer as close to factory slash dealership floor stock as you can get. And I feel that with as perfect as stock restoration that is possible, it will command the most interest of perspective buyers and highest price possible. There is lots of proof of this on the net. A good "original" will sell fast, were as a modified junker with a chopped up this or that, will just sit and fester on craigslist, those are the build it like you like specials, well most don't like what you like for mods.
Most people just see a good paint job and that is the main selling point for them.
Doing a good stock restoration is the most difficult thing there is to do. Just watch grave yard cars show, yeah they do some stupid goof ups here and there, but that Mark Worman guy really strives to do a good stock resto right down to the paint stick markings. To answer your question about the engine yes it will detract from the trucks value to the right person.
But engines are the easy part, its the sheet metal that is the hard part. If it is a patch work quilt of patch panels, its just a patched up junker and needs to be priced accordingly. If its a grandpa's truck that just sat in the garage most all its life, and didn't have a spec of rust on it, and just a new paint job that is way better than the patched up rust bucket. If the guy looking at it knows anything, he should be able to figure out what kinda condition its in. Also I have seen trucks advertized with big prizes that just have a nice paint job and everything under it is a mass of rust ie not a restoration. And meaning there could be lots of worn stuff under there.
Yeah when spending the big bucks on something the frame
better be in good shape too.