From my quick tests, it appears boosting the digital input +3 on my BD30 has returned my normal listening levels to -10dB. In addition A/B testing now shows a subtle but noticeable difference using DEQ. So I think for now this will solve my problem. But if Chris can confirm DEQ ignores input trims, that would be helpful so I know it's not a placebo effect.
It's still odd with 1.95 it re-running Audyssey drastically lowered my sub trim to -10dB down from about -3dB. I'm going to move the volume knob on my sub a tad and re-run Audyssey to get it closer to 0.