"We have extensively mapped the path of evolution that resulted in that life" just proves our sample set is statistically insignificant. One planet our of billions isn't proof of anything except what happened in our back yard. All life on this planet stems from the same root genome, and most vertebrates are tweaked variations on the same basic plan. The tiny bones in our ears are adapted from jawbones, for instance, and just because that happened here doesn't mean it's going to happen in the same way on a totally alien planet.
All true, but do you also question whether distant planets are round, just like Earth? I presume the answer is no, because you know that the laws of physics dictate (hypothesize really) that gravity 'works' that way. So, you're probably right on the small chance of an alien having Earth-like ears, but there is a very good chance that they have (biological) sensors to maintain an awareness of their situation and their environment. Given than an atmosphere implies a gas, it might thus be the case that one of these sensors has specialized in detecting pressure differences in that gas, similar to our ears detecting these in our atmosphere. Placing these slightly apart will then provide an advantage, as you can measure distance and orientation of the source more accurately. Moreover, curving the outer part of this sensor might amplify the signal, thus once again improving survivability. Linking to my previous post, we might want these sensors close to the 'brain', and on an effective and safe location: a head.
I try to keep it as abstract as possible, as we can't say much about how they are formed and evolved. So no, I do not believe the bones in their ears evolved from their jawbones, but I do believe that an intelligent and tool using alien can only reach that place in its environment if it high up on the food chain, thus having a good situational awareness (due to its sensors), good reasoning abilities (= a central brain-like structure), and a body to match its tool-making skill.
Sure, aliens in ST look a little too much like us to be plausible, but I believe it is much more realistic than the aliens that look like they came from a horror movie. It might be cool and all, but you don't become an intelligent space-traveling alien if you can't even pick up a screwdriver.