I ran AccuEQ again. I set the sub at about 1/3. I got these values: fr -12db; c -5.5 and sub -8.5. Not sure what to make of this.
Good.
It is interesting that your Center changed from -7.5 to -5.5.
That your L/R did not change and is still at -12dB only makes me lean harder toward my thought that these are "breaking" the room correction a little.
Your AVR is trying to compensate for their high sensitivity by attenuating the signal going to the Speakers. I'm guessing still that -12dB is the limit with which your AVR can make these adjustments.
My suspicion is your Mains are still louder than they should be to properly blend with the other Speakers.
Regardless:
Shall I forgo all that and manually put all three at 0? Then adjust to my liking including surrounds and heights?
No. Not unless you get a way to manually check the SPL setting for all your Speakers. If you wanted to go this route, you should bypass a free phone app and get a real SPL meter. But this gets tricky and might not be necessary.
Playing an LP afterwards and the sub certainly was on but not loud enough at all.
OK. But because the AVR set your Sub to -8.5, you now have some room to adjust that Trim level upwards.