The truth is somewhere between what Isaac and SacredWitness are trying to argue. Advantage does not always grant the same bonus, true. But it remains significant pretty much always because bounded accuracy ensures that the target roll on the d20 stays around the middle third or so of the bell curve in the vast majority of situations. This is especially true for the low level content that BG3 features so prominently.
Regardless, as pointed out in the OP, easily accessible advantage devalues too many class features. Larian can choose to change or replace them of course, but that's ultimately creating more work for themselves and also too many potential balance issues from further homebrew.
The solution, as has been pointed out multiple times on these boards, is pretty easy. Because 5e hasn't actually done away with all flat modifiers to rolls (see: cover system, which is currently missing from the game). All Larian has to do is replace the adv/disadv on height with flat modifiers akin to that subsystem.
