I agree that its a structural issue, though I think its set by the athletic commission rather than the UFC. Most prize fighting rules are set by the gov't rather than the promotions (for pretty obvious reasons given what a lot of promoters would allow if they could -- sharks with laser beams would be the starting point).
And I agree that some of the responsibility is on a fighter who goes so low they end up drained. However, some promotions are pretty bad about forcing the fighter who drained himself to fight anyway even if his opponent missed draining himself by not making weight (I'm not talking about Khabib here or even the UFC, but a lot of smaller promotions don't have back-up fights and put a lot of pressure on fighters to fight even if their opponent didn't do a real cut).
I also don't think Khabib is routinely gaining a material advantage, almost everyone at the UFC level is running the ragged edge of how much dehydration their body can take at weigh-in. Its more that he hasn't always had the science of cutting right. Missing by three pounds suggests either an illness in training camp (in which case the fight should be postponed) or a faulty procedure. I doubt anyone in the UFC intentionally misses weight, given how quick the UFC is to cut fighters.
Having said all that, the difference between cutting those last couple of pounds has always been huge even 24 hours later. And its worse now where IV isn't allowed to rehydrate.