My experience has been the same.
I've bought and sold some vintage instruments that were dogs.
Back in the day I had an untouched 58' burst that sounds like crap.
This was in the early 80's when they went for under $10K.
There was absolutely nothing wrong with it but it just didn't sound that good.
I have seen a bunch of 70's P & J's with ski jumps.
I own 5 (all 72 or 7 2 J's and 3 P's

that are reasonably straight but none are perfect.
Interesting idea Whippet, I have not encountered this but it certainly is possible.
Next time I have some time I will check with a dial indicator and/or a vernier caliper to see how close they are.
This may be worthless info on my part though as these all sound very nice (to me).
Am I the only one leery about buying a parts guitar or bass?
I'm thinking that Fender, Lakland, etc. wouldn't let their higher end instruments go out the door if they were dogs; or, I'm completely wrong about modern QC!