GM-
Let me see if I can confuse you a bit more.
If you tune the antenna itself for resonance, you'll check it at the feed point. That will make the antenna itself as efficient as it's possible to be. HOWEVER, as soon as you stick a feed line in, you are introducing some sort of reactance that will affect what the transceiver sees AND result in a mismatch of some type or another at the connection of the feed line to the transceiver. That mismatch MAY alter what the transceiver wants to see, to the extent that damage could occur. (Damage is unlikely with modern rigs, they have built in protective circuits that will cut back on power or simply shut down.) Therefore, tuning for lowest SWR as the rig sees it is the best possible way of getting rf to the antenna.
Each and everything that is inserted into the "space" between the antenna and rig represents a measurable loss of signal strength and some reactance of one type or another. Considering all the insertion losses and providing compensating reactance with a tuner (another loss, the tuner is an insertion itself.) All else being equal, it makes no difference if the tuner is internal or external, they are losses which are acceptable from the standpoint of getting rf out of the shack.
I sure hope I got that right. (I've put out incorrect info before on occasion. If this is grossly off base, someone will correct me, I hope.)
73
ghrit