I took this realisation to the extreme and decided to completely deprioritise classes in favour of homework and doing the reading in my own time. I figured the cost-benefit, at least for me, was much higher if I spent an hour doing as opposed to an hour listening.
This actually worked really well for me but that might also be because I often struggle with large classroom learning: the pace is either too slow and I get distracted or too fast and I can't keep up. But even when the learning is 'one-to-one' I feel like there's always the tendency for people to zone out and not raise an issue when they are either bored or did not keep up/understand.
I think you're right in that some of that might be the brain pretending that it understood when in fact it did not. Could it also be a social thing? Maybe because the other person expects you to understand and this causes your brain to try its best to believe that it understood when it did not.