It can be a difficult balance. While I don't specify how to make a part, I can't ignore what it takes to make a part. As you mentioned, different shops will have different preferences according to experience and equipment. Being aware of what a shop can do, a drawing can be tailored to those capabilites. Also, candidate shops' capabilites should be matched to the parts they are working on.
I don't see ANSI drawing spec entering into the discussion. We're not talking about specifying which tools the shop has to use to create the required geometry. We're talking about being aware of what a shop's needs and capabilities typically are, and taking advantage of them.
Your unfortunate experience with the lowest bidder seems to me to be an example of why price should definitely NOT be the only criteria for who gets a job. If the shop bid on a job that they couldn't do, then their price is not a useful measure of the most cost effective way to organize a drawing. That is, they failed to correctly evaluate the job. The data should be thrown out. In the specific case of holding .0005", that may be a case where a setup is actually added to the machining, because the machine that taps holes probably can't reliably place holes to .0005. So the part will have to be set up on another machine that can handle that job.
I thought for a bit about your suggestion that what I actually want is a separate drawing for machining and inspection. Maybe that's not what you actually meant, but I don't see how that would help anything, and I didn't mean to suggest it at all. Why would I want that? Machinists know that a part will be inspected to the tolerances they see on the drawing, so they make sure it's right before they're done with it. I don't see any purpose in disconnecting that. I must not be clear on what your trying to say there.
One might argue that tolerancing should be derived solely from fit and function, and that reference dimensions can facilitate simpler setups. I think this is reasonable, but it makes more work for everybody. The drafter has to add the extra dimensions, and the machinist has to reinterpret the tolerances for his setup to be sure that his part will pass inspection. Everyone I know is happier when I give them toleranced dimensions they can work to and the part will fit and function. They are free to make the part however they want, but I try to make it as simple as possible.
I don't think this is unique to our shop, or simply a preference of a few stubborn machinists. We have a lot of guys from a lot of different backgrounds, and I get similar feedback from all of them on what makes their life easier.