I do think something is lost in the middle somewhere.
The system does not calibrate for specific sources. The source is immaterial. Each speaker can be individually calibrated because there is no overlap of sound... except for the subwoofer.
See, if the source is immaterial, why is there "no overlap of sound except for the subwoofer"? I really haven't followed your logic here yet.
I'm not aware that Audyssy levels the sub flat and then levels all the other speakers flat regardless of their F3 finding. If I am wrong and that is exactly what it does please let me know (I think that would result in a volume increase at the crossover point).
No, I never said that. It will calibrate for everything ABOVE the measured F3. Again, this doesn't mean you HAVE to use the full bandwidth that it calibrated for (I don't, and most people don't).
Also, I need to point out that the use of the term "flat" can be misleading. Again specific to individual receiver companies, there are a variety of Target Curves. The Flat is indeed flat, and the other most common one used is the Reference (Audyssey/House), that has an HF roll off (not flat). THEN, there are even more, such as the curve designed by Paul Barton (PSB) for NAD, or Fronts (seen that with Marantz at least), and for all I know there could be more. That's already 4 different target curves off the top of my head.
I can't figure out why you would ask about a volume increase at the xover point. Remember, it is the receiver's bass mgmt applying the xover, whatever the slopes, not Audyssey. The xover point is chosen finally by YOU, and the the bass mgmt will implement the slopes.
Is, at the end of the run, EQ applied to the sub for frequencies well above the set crossover?
I assume it calibrates high enough for all intents and purposes of the typical subwoofer. The bursts that Audyssey uses for calibrating go up pretty high, and I hear some funky stuff from my subwoofer that I've never heard with any bluray disc, ever. Since I use XT (8 positions), that is 800 bursts just from my subwoofer that my Audyssey unit is measuring.
My subwoofer is crossed at 80hz. Still, since xovers are not brick walls, I leave the LFE LPF at the maximum of 120hz available with my Onkyo.
If I could, I'd also add a HP to my subwoofer with my Crown's BandManager software, but I can only set it starting at 20hz. Ideally, I would have it around 15hz, plus minus, therefore no subwoofer HP for me. Though I'm not too worried about it, as I never listen to reference level.