Exactly. Some of the best FM and EM programs are lesser known, because they don't have to compete with the well known IM and surgery programs. Depending on what your goals are when you ultimately go into residency, you may want to train at a more unopposed program, because you get to do more, and you have to figure out how to do more with less (depending on how the program is structured). On the other hand, if you're at an EM program with good peds and IM people, then you can learn a lot more from them. So it's a mixed bag.
You'll also see a heavy regional bias. The thread above lists only east coast programs as the 'top' pediatric programs, but University of Washington, OHSU, and Colorado are all also top programs, they just tend to recruit more from the west coast, so it's more difficult to match there if you go to an east coast school (which by the numbers, more people do). And there are lots of reasons for people wanting to go to less well known programs (couples matching, wanting to be close to family, wanting to be in a smaller program, etc), so just because they aren't going to a well known program doesn't mean that they aren't capable of doing so.