I also have a similar doubt. I completely understand this explanation of yours. But my doubt is with regard to YPAO. If it believes that there is no sub, would it not set the crossover lower (say 60-65hz), so that the "large" front speakers can handle as much of the bass as possible?
And therefore conversely, with the sub-connected, should it not automatically set it higher (say 80hz), so that even some of the notes which are within the rated ability of the fronts, but which would probably be handled better by the sub, (such as perhaps the sounds in the 60-80hz frequency, when you're talking about bookshelves), can be handled by the sub, and the fronts need not struggle with them?
By default, Yamaha sets the front speakers to large and the crossover setting to THX standard of 80Hz. This is whether there is a sub or not.
When the front speakers are set as large, you will usually find the sub option absent. In other words all frequencies are sent to the fronts. This is what I am used to, for example, in Onkyo. What surprised in this installation was that YPAO recognized the presence of the sub, and in spite of that, assumed the fronts to be large. So I was forced to manually set the fronts as small.
In the present case case, even if the PSB Alpha B1 can go down reasonably to 70-75hz, if the sub can handle the 60-80hz spectrum with greater comfort, would it not be better to leave the crossover at 80hz, rather than set it at 65hz. For example, you mentioned that the B1s are comfortable down to 70hz, so presumably 65-70hz (for the sake of example) is an area where they are not comfortable, and in such a case, would not setting the crossover at 65hz leave the 65-70hz frequencies inadequately resolved/reproduced?
Maybe my explanation was not enough or was badly worded (I shall edit it a bit later), but I have done exactly what you are suggesting. The Alpha B1s can actually go down to 65 Hz according to its specifications. So what I did was give it a leeway of 10 Hz, and set the sub to take over from 75Hz. I actually tried from 100 Hz downwards. I found the sub's sound to be a bit largish (booms and echoes) in the 75 to 90Hz range. I found the Alphas handled these frequencies much faster and they also died faster. I found the crossover at 75Hz to be the best for my ears. You are suggesting 80Hz, and I chose 75Hz.
I am very sensitive to sound that booms and echoes, and I want the drums to be sharp and of very short duration.
There is no hard and fast rule. For example, today I was experimenting with another set up where the combination was Q-Acoustics and a EPOS sub. Here the sub was set to take over at 100Hz and a Phase offset of 135 degrees. Both zero degrees and 180 degrees, brought in boominess that I don't like much.
I hope it is clear now. As I said the crossover is a combination of the specifications and capabilities of the front speakers as well as how the sub sounds. Many people like the large and boomy sound and for them, 100 to 120Hz may be an ideal setting. If you choose your fronts carefully, you can actually maximize the load to the fronts, and make the sub handle only the really low frequencies.
Cheers