I like this idea in theory (especially as you suggest giving rid of height adv/dis), but there'd be some difficulties. Currently, the game uses LoS to determine if it is even possible to hit someone: i.e., only caring about Total Cover. So to adapt your suggestions, they'd have to change that. Okay, sure, now characters are "see through" for the purposes of targeting other characters and the game counts how many characters your line goes through when calculating AC.
But Larian currently allows you to target different parts of character models to determine if you hit (If i can draw a line to someone's head but not their torso, Larian allows me to shoot firebolt at them without penalty). How is this implemented with cover? Does the game have to check what percentage of the target is covered by another character(s), drawing all the possible lines of attack? Not sure how resource-intensive calculation this would be, but at the very least I could see players complaining about unfairness if they disagreed with the assessment. Unfortunately, determining if you're "shooting through" another creature is easier in 2D grid-based combat, of which this game is neither.
I'll provide a compromise suggestion, where height always give +2 to attack and low-ground always -2. This is both simple and not as powerful as the current adv/dis, and sort of approximates the scenarios you brought up. If you're on high ground (rafter or cliff), the enemy probably can't see more than half of your body due to there being terrain in the way...
