While I can understand more sensitive speakers being set into the negative, that would be relative to the speaker set as well as distances from MLP. Seems odd that they're all -5 or greater rather than one set being more the baseline and closer to zero. Might have to go dig around Audyssey zendesk and see if there's any info on that. I wonder if that they're in-wall and missing some usual reflections if that's part of it.
Yes, looking at your sub manual they do indicate you should still max out the low pass filter on the sub to 160 even when using the L/LFE input (so in this case the sub apparently doesn't cut out the low pass circuit automatically as some do). I'm not clear on what you set to 100 if you did this and the fronts are set to cross at 80 (your speakers are all the same so I'd just use the same crossover for all of them). In any case, your sub only has a low pass filter, not a crossover (which is both a low pass filter and a high pass filter working together).
I thought you were just using the phone app as a backup measurement. If you did want to do manual setup I'd recommend a measurement mic like the Dayton UMM-6 or miniDSP Umik-1 along with REW (Room EQ Wizard) for software.
Seems confusing to me as well. My sub is a Klipsch reference R-12SW. The input is a single line and on the L/LFE.
The manual (skimpy) says to set the low pass filter knob on the subwoofer to 160 Hz and then set the crossover in the AVR to the same as the front speakers (80). I set it at 100 instead.
My room is purpose built. Large, 9' ceilings and fully insulated for sound dampening. Maybe that is why the Audyssey set all the speakers to a negative value ??
I used the phone app just to see what it was doing but the Audyssey setup set the levels.