Dave, I totally agree with you on the case you just presented of the yagi that has been optimized for a particular parameter (gain, for example)! If you've got the performance where you want it and you don't mind matching it with a network, then leave the antenna's performance alone and match it externally. On the other hand, if there is some reason that tinkering with the antenna first to improve the match is of high importance, then do it that way.... :-)
My thought is to use whichever approach gets you where you want to be with the best path to success.
Tom AE5I