well, your speakers are fairly efficient if ~ 90+ dB.
by contrast, mine are magnepans @ about 85 dB and all 7 channels get boosted by MCACC. the heights are small martin logan motion 4 bookshelves and they actually get a - 4 db cut, IIRC.
if you aimed the mic directly up to the ceiling, not tilted, there was nothing blocking or in the way so they had a clear line of sight to each speaker, and the Pioneer didn't give any channel a boost, then what it's saying is: to achieve reference level volume no channel required any boost and some actually a cut. your volume seems to be in accordance with the calibration reference level and it is what it is.
there's nothing preventing you from manually giving the levels a boost, as long as you maintain the same relative dB difference between every channel.
what's interesting is that you say the channels aren't mostly at 0 dB but when you choose a un-calibrated preset, it sounds "louder". this may be due to a particular freq band that got boosted, say the bass or treble ends, so the midrange, dialog region, sounds weak by comparison.
if your speakers are close to your listening seat, then it may be compensating for the short distance.
it's all relative and overall volume will vary from room to room, speaker brand to brand, and unique to speaker distances.
I have found, with my magnepans, my typical volume is -10 to -4 dB on the volume dial but I know there are owners that listen in the -25 to -20 area. it just depends.
so you might want to take a look at the EQ settings, see if mid bass, upper bass & treble levels are boosted over that for 500 K, 1K and even 2 K and judiciously adjust to taste.
you might also want to look at the orientation of the center channel speaker, make sure its not firing over your head or aimed more toward your feet
it should ideally be aimed where your head will be and not straight out into the room or angled too far down.
to me, it kind of reads that its the dialog mostly not necessarily overall volume level that's your problem. so look at 1Khz for sure.
it could also be a problem with the mic, that is possible. I also know that over the years, MCACC has been tuned differently. my old VSX-59TXI set all channels exactly 6 dB higher than the SC-09TX so to get equal apparent listening volume, the volume had to be set ~5 to 6 dB higher. the SC-68 is different still from the SC-09, it's l/r channel levels are only +2 dB while the SC-09 set them at +5 and the 59TXi was ~ 8 dB. I suspect the different preamp outputs Pioneer uses are due to tuning differences & possibly even different amp gains as their amp designs changed.
see if tweaking the EQ helps with the dialog. you might also want to re-run it from scratch in case it was a measurement problem.
it's always possible the receiver has a defect but not likely.