How does "bottoming" a tremolo effect tone?

[SemperRhythm]

For example... on Fender Strats with "vintage" tremolos (six screws instead of 2). My peavey has the same style bridge and was "bottomed" when I bought it, meaning you can lower the arm but can't raise it because the tremolo is resting flat on the body. I do like this though because on the rare occasions I drop-D, I don't have to retune all the other strings and it seems to be very stable (staying in tune).

Anyway... how does the tone differ (if it does) from have a tremolo in standard position as compared to "bottomed"? I'm asking because I'm soon to have my Highway 1 Strat and plan to bottom the tremolo and want to know so it helps on pickup selection.

Thanks,
Nathan