Local widgets & theming yes, although generally we ship with our own themes by default as we make VFX apps, and the last thing artists want is bright UI to distract them.
I don't believe there are general UX guidelines for Linuxes, but for things like notification popups, system tray stuff, yeah, we do all that natively to the distro through Qt (DBus handles all that transparently within Qt very nicely).
We ship Qt as shared libs with the binaries and all dependencies we need system-wise statically - i.e. zlib, libpng, libjpeg are statically linked. For things like embedded Python, we have to do the same on OS X anyway, due to different python and zlib versions per OS X version.
As for Qt and OS X regarding nativeness - I keep hearing this, but I never see any good examples. I agree it's possible to create Qt Apps on OS X that looks crap, but it's also possible to make them look native as far as I'm concerned. The only thing I can remember not being able to easily do in Qt regarding OS X widgets is the horizontal grouping of side-by-side buttons in radio-button fashion. But it's easy enough to knock up a QWidget subclass which replicates this. But admittedly I don't think I've tried to replicate every possible OS X control/widget...
I think what might be the most difficult part of making a Qt app on OS X look native is the layout and spacing stuff, which generally does seem to be a bit crap within Qt on OS X.
I can have the same code to do a side-panel with edit values in a panel, and it looks great on Linux and Windows:
http://imgur.com/kUI90ry
on OS X:
http://imgur.com/yqigBdw
and the spacing and padding is all over the place - so I have to add a manual style-sheet to get the padding and spacing right, which is crap (image above is without extra stylesheet). So I'm not saying it's perfect or easy, but I think it is possible.