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Not sure, but it seems like we're dealing with two different types of time travel here. In the initial case it was only Desmond's mind that traveled from his body from the different points in 2004 and 1996. In the second case there seems to be actual physical time travel involved, as none of the people were actually on the island in 1954 and so on.
With regards to Supreme, I am guessing the reason Desmond is the only one who experienced the "side effects" on the island is because he was already prone to them, and so when they went off course a bit it triggered his mind to unstick in time. In the case of the survivors, seeing the light when Ben turned the wheel may have been all that was necessary for their type of time travel.
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