IMHO, even if you theoretically could achieve a technically (not objectively i.e. visually) higher quality version of a clip through Compressor, I highly doubt the task of endlessly fiddling with GOP structure, P-frames et al to get there is worth the minute difference in the end. The encoder is the exact same in both cases and delivers very acceptable (if not by today's standards ;) ) results either way.
Using the standard settings (i.e. without fiddling) in either would give the same results from what I've (unscientifically) tested.