I know the answer to this probably is the S.E. staff, but what if the community is not happy with the design they apply? Can we petition a change?
I'd rather concentrate on graduating rather than worry about this.
That said, I know that during previous graduations the site design was vetted with the community and feedback was taken into account. There is no reason to suspect we would be different here.
SE has the final say, but there is no reason for them to force a hated design upon the community.
We provide input here on Meta, SE (more specifically SE's designer) does the final. See the previous questions on this topic - design. The designer (Jin at the time, it's been a while) chipped in some.
I do hear rumblings that we may get a design without graduating, but it was part of a pretty hedgey email about beta maybe isn't beta etc etc... Don't let that stop you from trying to boost site traffic.