It does sound like at least some vets are overly anxious about OK-ing a horse without finding something that could be a caveat. I don't know what the answer is. What we want is to know if the horse is currently suffering something, or if they are prone to break down bacause of an obvious defect. But ALL horses have the potential to be injured any time anywhere, it's part of the game of athletic sport. No horse is a perfect specimen in all areas of conformation, all horses could be designed better somewhere. It's OK to point out conformation areas that are not ideal and describe how that shortfall might limit some expected activity, but all that needs to be taken as good background information to be aware of in moving forward in training and conditioning for the sport, not necessarily a reason to back out.
We didn't do a pre-purchase exam on Cyn... we just took the shot because at her age and usage we wouldn't expect anything pre-existing to be wrong. IF we had, and IF the vet would have seen her stifle issue, would we have declined on her? I don't know. It's really minor.
As for trying to set ground rules for vet checks, I think you'll lose buyers... I'd be leary about a 'no vet check' rule, even if I wasn't planning to have a check. But I'd be happy enough and would find it useful to talk to your vet, because I think the history of treatment is valuable, and I would assume vets would be honest. They aren't going to outright lie for any one customer's business.
I'll say this, when I had my vet out a couple weeks ago to do shots and a soundness evaluation on Bay, and Bay was so hot-to-trot, he said, "If this was a pre-purchase exam, I'd approve him without even wondering if he had Navicular".
The best thing might just be to insist you be there when he does the exam and gives the report, so you can have input. Just a thought.