...As noted, in your post, it is a good idea to always try to keep subwoofer AVR trims in the negative range--ideally at least -3 to -5. But, as I understand that, and as I quote some audio experts as saying in the subwoofer guide linked below, that is because you specifically want the voltage which powers your subs to come from the subwoofer amp and not from the AVR amp. The higher your AVR trim level is (and particularly above about -3) the more it is your AVR amp which is powering the subwoofer. Keeping the AVR trim level low for the subs, and using the subwoofer gain control to increase the sub boost, keeps the signal cleaner and helps to prevent clipping or other issues.
But, the situation is different for the regular channels. They are actually supposed to be powered by the AVR (or by an appropriate external amp) and there is nothing inherently wrong with having positive trim levels for those channels. This isn't really something that is subject to user control anyway. It will depend entirely on the relative sensitivity of the speakers, and on their distance from the MLP. When an AVR runs a calibration routine, using a 75db test signal, it will measure the FR of each speaker as it is at the MLP. And, it will set trim levels accordingly.
With a sub, if you don't like your trim levels, and want them to be deeper into the negative range, you can easily get them there by raising the gain control on your sub. That will increase the measured SPL of the sub and cause the automated calibration program to set a lower corresponding AVR trim level. But, we don't have a separate amplifier to allow us to do that with our regular channels, so our AVR trim levels for those channels are whatever they are. And, that is usually fine.
In my room, for instance, one pair of my speakers are (deliberately) 21' away from my MLP. There is no way, that I am getting solidly negative trim settings from that distance. But, that's okay. As long as I exercise reasonable bass management, I still have plenty of headroom to play as loudly as I want to. People who really want to play at Reference (0.0 MV) or higher, need to be mindful of both good bass management protocols and of the sensitivity of their speakers. But, for the vast majority of HT systems (and users), Reference volumes will be much too loud anyway, and the speakers will be perfectly capable of playing with sufficient headroom, even at positive trim levels.
Again, the whole positive/negative trim level dichotomy is based on the advisability of using subwoofer amplifiers for the subs, rather than AVR amplifiers, and it applies only to the subs. Of course, if someone has excessively high trim levels for the regular channels, and is exceeding their capabilities, then larger, more sensitive speakers may be required. Horn speakers are especially capable of producing high SPL, for instance.
I hope that this explanation is helpful.