1. Yes, absolutely! This is the point I've tried to explain several times, apparently unsuccessfully. I'll try an be as absolutely clear as I can: The basis of all level calibration for 5.1, 7.1, etc., is the main/screen speakers. Everything else, the LFE/sub and surrounds are calibrated relative to that main/screen speaker calibrated level. The -3dB for the surrounds (cinema only) and the +10dB in-band gain for the LFE (cinema and home) are -3dB and +10dB relative to the screen/main centre speaker, which in the theatrical specification is 85dBSPL (C). And to be clear, this 85dBC is the level measured with an SPL meter with the main/screen speaker outputting 20Hz-20kHz pink noise (at -20dBFS). Our LFE is level calibrated to +10dB
in-band gain relative to our main/screen speaker. The "In-band" part means that our LFE/Sub should be outputting 10dB more 20Hz-120Hz than the amount of 20-120Hz our main speaker is outputting. The issue should hopefully now be obvious, our main speaker is not outputting 85dBC of 20Hz-120Hz, it's outputting 85dBC of 20Hz-20kHz. If we remove the 121Hz-20kHz output of our main speaker (so that it's only outputting our required 20Hz-120Hz), it's output level will obviously be lower, it will be approx 81dBSPL and our sub is then calibrated 10dB higher, which is about 91dB. In practice, we wouldn't try and "remove the 121-20kHz", we'd just use an RTA to measure the 20Hz-120Hz portion of the main speaker's output. In other words, your equation should read: "85dBC - (the 121Hz -20kHz band) +10dB = 91dB".
2. This is where it can quickly get confusing, with your sub playing double duty, as I explained to Steve999 in the second paragraph of
this post. To adapt the official manual LFE calibration procedure for a bass managed system, I would first sort out the bass management part of the equation. With say your centre speaker, use a sine sweep (or 20Hz-20kHz pink noise) and RTA software, and set the level of your sub so that you have as flat a response throughout the spectrum as practical, the main goal obviously is to equally balance both sides of the crossover point between your centre speaker and your sub. Once achieved, level calibrate your centre channel/sub combo to (say) 78dBC with 20Hz-20kHz pink noise at -20dB, using the "C" weighting, "slow" response on an SPL meter. Without changing that level (or the pink noise signal), use your RTA software (set to 1/3 octave bands) to take a 20Hz-120Hz plot of your centre/sub combo. Now take band-limited (compensated) 20Hz-120Hz pink noise, output that through your LFE channel (to your sub only) and take an RTA plot of that. Finally, EQ your LFE channel (NOT your sub!) so that each 1/3 octave band is 10dB higher than the corresponding band in the (20Hz-120Hz) plot you made of your centre/sub combo. However ...
3. I'm not sure but I would say probably not. If you try and achieve this by software in the digital domain, it has to be done the other way around. IE. You can't apply the boost to the LFE channel, you have to apply a reduction to all the other channels. Typically, you would accomplish the +10dB in-band LFE gain in the analogue domain. You can't just increase the LFE channel by the required amount in the digital domain. What would happen in the digital domain if the LFE channel on a particular film peaks at say -1dBFS and you try to add say 6dB? As you can't have +5dBFS what you actually get is a nasty clip! Even if you were considering the calibration method I explained in point #2, that final 10dB per band LFE channel gain would have to be done with an analogue EQ or, you'd have to devise some way of applying it's inverse (reduction) to your main/screen speakers.
I know the above is confusing but again, it was never designed for consumers. In fact, it wasn't even designed for us sound engineers, it was designed by Dolby for the sole use of it's own technicians! Part of the licencing contract which allowed film mix stages to produce films in 5.1, 7.1, etc., required that Dolby's own technicians calibrated the mix stage and the mix/sound engineers weren't allowed to touch it! The problem with multi-channel music production is that it's relatively rare (outside of the film music world) and the music engineers sometimes have the same lack of understanding of LFE calibration, even some of the most respected engineers. So, even if your LFE is correctly calibrated, you maybe trying to reproduce music which isn't! As a general rule, for most people, I would advise that you let your AVR deal with it.