I'm sort of the opposite. I've played with some great players but the ones who are self taught and have chops are the ones I expect the most from. I expect them to be able to play complicated material by ear, to find and sing a missing third part harmony without coaching, and to have recordings of most popular material at the ready in their own heads. That's been my experience, hands down, with the best self-taught players I've worked with. And they are rare.
The communication issues are an interesting wrinkle. When you're playing from your head and ear, those things just don't come up. Why? Because you already know from your ear what you're supposed to be doing. Clarifying conversations are rarely even needed. Normally if there is a conflict, it's enough to clarify the root of the chord, which is a pretty simple conversation to have. I don't need to hear what chord form it is, my ear already knows where to put my fingers based on what I'm hearing.
Best player I ever worked with had both; was a classically trained guitarist with a great ear and could hear anything in his head that you wanted him to spit out. I sure miss that guy.
I edited this to emphasize chops. That's because I think there are people who go a self-taught route but maybe don't have a very good ear, and these people can sometimes get into trouble. Maybe they think they know more than they do (heck, maybe I think I do, too). As I said in the beginning, I don't judge on method of learning, but what you can play. And once I know you can play, if I find out you're self taught and you're playing complicated stuff, I know you have an ear, and I'm going to expect a lot more from you. That's when my expectations begin to build, but in a good way. I'm excited to find good players with an ear like that, no matter how they got there.