It's very possible to write a Qt app that looks and feels fully native
in GNOME/Unity. And I believe Qt apps will look better outside of
GNOME than GTK ones will. Also there are a lot of good apps available
in KDE that may not be available elsewhere in Ubuntu (kdeedu is but
one example).
You are very welcome to write a Ubuntu HIG and propose it. If you can
attend an UDS, that would help a lot with promoting your proposal but
UDS isn't necessary. Ubuntu community members can get involved in
nearly all parts of the Ubuntu development process, limited only by
their time, abilities, and desire. Please don't feel that you have to
be a Canonical employee to contribute.
The Linux and open source community is much more than just Ubuntu. You
might also want to help GNOME with updating their HIG for GNOME 3. I
imagine a Ubuntu HIG would be the GNOME HIG with a few differences of
opinion anyway.
I'm not sure how the formatting of this will look, but I'll go ahead and say I want to tackle paragraph one as one issue and 2-3 as the second.
So, re:Qt app. Yes, it will behave natively, there is no denying that. But it has to be coded very specifically to do so. If just a standard Qt app, it will pull in icons for it's app menu (something no GTK apps I can think of do) and any buttons will have items underlined in them for keyboard shortcuts by default (Someone please correct me on that if I'm wrong) which makes it one of those VERY slight, but noticeable things that make them stand out. Would the average user pick up on that? Likely not. But an inconsistency is an inconsistency. (Note, I'm not discounting the inclusion of Qt in Ubuntu, just that there should be a definitive toolkit for "definitive" apps)
Re: HIG. I cannot make it to UDS (though I do wish i could). It is possible to create a guideline, but I'm under the impression that it would require some input from Ubuntu designers to define what should be and what shouldn't because they are in charge of the (C/c)anonical defaults. Without their input, it comes down to guesswork on how things should be handled in an Ubuntu App. However, once their general "rules are established, it would primarily be a community thing to run the ball to the goal line.