I top wrap some guitars but not others. I definitely notice a difference in feel bending the strings when they're top wrapped though.
As for the physics, it makes sense that at a given pitch, the same scale length requires the same tension regardless of the length of inactive string.
But I think when bending notes, you're increasing the tension of the full string from tuner to tailpiece, not just from nut to bridge. So to bend a whole step on a slightly longer string length (top wrapped) you need to bend it just a hairsbreadth further. This, I think, is enough to give it that slightly different feel - especially when it comes to small amounts of bend as in finger vibrato, or even the very slight deformation involved with fretting notes.
This to me is where the difference is most evident. The same thing would account for the difference in feel on a toploader Tele vs a string-through one, or a trem Strat vs a hardtail.
I'm not 100% sure this is the actual principle at work here. But as the saying goes, I'd argue it over a beer.