The trick on replacing traveller track rivets is two-fold:
1) Make sure the track is held down tightly to the crossbar. This can be a simple as tightly wrapping a piece of line around the crossbar / track assembly. The rivets will not
pull the track down.
2) The nose of the rivet gun has to seat firmly on the top of the rivet, which in turn, has to be firmly seated in the countersink. Most rivet guns will not fit into the track, so you can either stack washers on the tail of the rivet (OK) or modify the nose of the rivet gun to fit in the track (best).
A preventative measure is to deepen the countersink in the track a little (emphasis on "a little") before setting the rivets. That will ensure the rivet heads are below the bottom of the track.
After the fact, you can grind down the protruding rivet heads with a Dremel tool. Just be careful. Aluminum (track) is way softer than stainless steel (rivets).
Jim, you're right that you don't have to worry too much about the rivets on the end. Until you jibe in heavy air and the traveller hangs up on a rivet head - on the wrong side of the boat!
(that's happened to me on my 17 and the result was an unexpected swim)