Hi, Javier.
I'm new to the plugins myself, but from what I've seen; with Monoliths on everything including the Master Bus, it needs to Learn from the whole song rather than just the quiet/loud sections, then after you Mix them all, it needs to Learn the whole song a second time to fully balance the loud and quiet parts, before the final Mix again... That should resolve your volume imbalances, I'd think?
As for controlling a volume bump during song sections, there's a YouTube video on their channel showing how to do that, by triggering the bump with a muted noise signal during its choruses, would that help you?
