UI redesign will most certainly take place on the homescreen, the launcher, the dialer, etc. In other words: in it's own seperate applications, this wouldn't conflict somewhere because it's done quite frequently.
Android is themeable quite nicely, so even changing the standard dialogs from one style to another _should_ work.
My own concern here is that some developers probably have written their own UI code and some custom hacks. But we'll see about that.