Hello paulbroke :wave: Nice avatar! 😉
Naturally you have excellent taste in speakers! Congrats! Let's see some pictures too!
Personally I've never much luck with Apex and Pioneer (LX83 and LX85) while others love it. Obviously someone more knowledgeable on MCACC should answer your question but according to everything I have heard this system only calibrates down to 62Hz regardless and that is it, hence the limitation. Nor does it EQ the subwooferchannel, if I am not mistaken. One would think Pioneer could have updated MCACC to handle these things better. Seems Audyssey, ARC and YPAO might be more advanced in those terms (doesn't mean you can't get an end result that suits you though).
If you set a crossover to 80Hz (preferred with Apex) almost all the bass below 80 goes to the sub; some bass is still output from the other channels due to the nonbrickwall nature of the filter, but it rapidly attenuates with decreasing octave (rate is dependent on the slope). Same goes for audio above 80Hz being output from the sub, at that setting -- there is some, but it's rapidly attenuated the higher you go above 80 Hz. The thing is, I don't think MCACC takes speakers size/crossover to sub/slopes into account at all when setting levels. It just outputs pink noise full range from all channels sequentially. The only place the size/crossover comes into play is when Acoustic Cal EQ 'decides' which frequency bands to adjust. It won't try to EQ bands below the crossover point.