I've never played in a PnP campaign where the DM scaled a monsters CR. If the party is too high of a level for goblins, for example, they don't make standard goblins stronger, they add in higher CR monsters like ogres, worgs, hill giants, etc. That isn't the same challenge scaling we are talking about here. We're talking about the system like in Skyrim where ALL enemies are you level, whether they are elite guard or lowly peasants. The level scaling that BG3 SHOULD have is where, depending on the difficulty you choose when you start your game, they give you monsters of the CR that you picked. I don't want to see normal goblins at level 5 that are CR 5. If there is a goblin boss, or goblin shaman, that is stronger than a standard goblin that's cool-beans...they are. but not the scaling we are talking about here.
One is easier to do than the other. But it really doesn't matter which method is used. If there is some algorithm that can magically add in the right types of monsters to increase the challenge then that's scaling.