Sam’s knack will actually only work on humans – and it won’t work on any human that got cursed by Celeste! So he can’t tell if Dean is looking at him in Brothers Lost, which is a good thing because it also means that Dean can’t screw it up by glancing over at him.
If a human shrinks down by another method, he will still be able to tell if they are watching. It is only humans cursed by the method Celeste uses that are an exception to this rule.
Truthfully, I came up with the ability during Taken. So yes, he does have it, but it didn’t start to show up until then. It’ll be more prominent in the other AUs earlier, but you can see it from Taken and on. In fact in Adventures at Bobby’s, Sam discovers that Dean does not set off his danger sense at all. He can tell that Dean is looking, but he can also tell that the gaze on him is safe.