Apple’s modifications are a definite improvement to my eyes, mostly because they thicken up some of the wispier glyphs from DejaVu, like the underline and period. There’s a great comparison over here.
One thing that bothered me, though, is that they turned the zero into a 1980s-style “slashed circle”. Unhip, daddy-o! Naturally I searched for a font editor, and the best one I found was Font Forge, an old Linux app ported to the Mac but still requiring X11. So that’s two ways OS X is borrowing from Linux for font support. What’s up with that?