When I hear people advise others that it is all "in the presentation" I tend to want to say "no chit Sherlock." Of course when the fish sees the fly, it sees it as it is presented. But the proper way to present a fly varies according to the fly and the conditions. Sometimes a presentation that seems unconventional works better than the prescribed presentation of some expert that for the purpose of simplicity, has recommended a certain presentation for a certain generic stream circumstance.
I do think certain presentation options should be tried first depending upon the stream circumstance, but if it fails to work, try something else. For mayfly dries, drag-free drifts should be tried first, for streamers, moving downstream slightly faster than the current, for emergers, lifted, nymphs, dead-drifted. If you could only choose one presentation technique, a generic formula like I just mentioned may give you the best odds, fortunately, you do not have to settle on a single technique for a given fly.
So in sum, presentation does not refer to a single manner of presenting the fly. We should emphasize proper or appropriate presentation and be willing to experiment in any given circumstance to find it.