Konsole,
Your post has more than one theme. First I'll respond to the question "how can they put my kid at 3rd base without even having seen him or the other varsity players in tryouts?" Well, rhetorically speaking, how did the coach know which kids to select as varsity players, since the chosen kids didn't do anything at tryouts? The answer of course is that the coach has already seen them play or is taking the counsel of others who have seen them play. The players' performance during the previous entire season is far more indicative of their ability than anything that can be gleaned from 3 hours of tryouts. If you are willing, as you seem to be, to accept the wisdom of the coach in selecting your son for varsity, you should also be willing to accept the coach's choice of position for your son.
"Why are they going to play him at 3rd when his best position is SS?" The most likely reason is that they judge that the team will be stronger with your son at 3rd rather than SS. Their thinking may be that the kid who is going to play SS is a little bit afraid of the ball, or that your son has the quickness of mind and body to field bunts well, or perhaps the other kid is simply the better SS. It isn't relevant to the team if your son is somewhat stronger at SS than 3rd.
"But he wants to play SS and is disappointed!" Probably 10 other kids on the team also want to be the starting varsity SS. Be glad he made varsity. Be glad he'll get to play. Be glad he gets to play 3rd instead of 2nd.
"He just wants a chance to earn the SS position." Every practice and game he plays, he'll be getting a chance to show his ability. If, as the season progresses, he emerges as the superior infielder, the coaches will decide that the team will be better off with him at short, and he'll get moved there.
Finally, please don't worry about being "labeled." If he really has the attributes necessary to play short, and is better than all the other kids, he'll get to play short in high school. Even if he played left field in middle school.