Nick, that's the best explanation of the phenomenon I've ever seen. That description of the PBY was pretty accurate. For a given cruise power setting, say 550hp, depending on cruise weight, you could indeed squeeze extra mph out of the thing by climbing a couple hundred feet past the cruise altitude then begin a gentle descent to cruise. I did familiarization on the C-46 our company owned, before it was sold, and that technique worked for that aircraft as well.
The single Otter was another aircraft that needed a certain touch. Loaded, this aircraft was very tail heavy, particularly on floats. The trick was to add a few degrees of flap. This seemed to raise the tail a little, and the aircraft flew better. Added bonus was a reduction in CHT's.
Your first paragraph, about water operation, is also bang on. You could sit there all day using great whacks of power, going nowhere fast, if you weren't 'on the step'. To get 'on the step', hold the stick full aft, add take-off power and wait until the nose rises as far as it will go. Ease the stick forward and you will feel the aircraft begin to accellerate. You then allow the aircraft to reach flying speed, and fly off the water in that attitude. If you want to establish a 'step taxi' attitude, once the aircraft is planing, reduce power to a setting that'll maintain the planing speed. Then ease the stick forward until you feel the aircraft begin to decellerate slightly. Be very careful doing this, as the aircraft becomes directionally unstable.Ease the stick backward again until you feel the aircraft accellerate and it regains the lost speed. Note the attitude where the aircraft planes most easily. Voila, this is the step attitude for that particular configuration.