Your measured distance (delay) with MCACC may differ from your manual measurements due to room effects/speaker placement somewhat....did you measure with the microphone placed where your ears normally are? Subwoofer distance may not match up particularly due to the additional processing time in the sub's amp, and can sometime benefit with further experimentation with the setting. Have you tried flipping the phase on the sub back and forth to see what gets you the stronger response? Experiment with your manual settings vs MCACC, after all in the end its simply preference.
I'd still not use the low pass filter on your sub and keep that set to it's maximum value, altho some subs using an LFE input will do that automatically. Cascading filters together (the one on the sub and the one in your avr) is not generally recommended but hey if you like it, go for it.
I personally don't use double bass features myself, nor recommend them. You might elevate the subwoofer channel level in the avr as another way to bring up the bottom end but without the doubling up of frequencies in the speakers that double bass features can do, many do this. Even large floor standers I still set to small so I can utilize my more-capable subs. You may benefit from a more capable sub, too (how large a space does yours need to pressurize?).
