The easiest solution to the missed companion scenes would simply be to have them queue up; only one character sequence can play per long rest, but they queue and wait, and one will play each long rest until they've all played out or caught up, and you never miss one... So supposing you've done enough things to unlock three of Gale's scenes and two of Shadowheart's, and three of Astarion's, but you haven't long rested at all yet this game... over the next eight long rests, even if you spam them one after another, these scenes will play, one per rest, in order, with some way to determine character priority, and after that no more will play until you've unlocked more.

As far as I'm aware, that's how a LOT of games handle progressive character interactions, and it's perfectly functional...