Why don't make mainwindow.ui?
In almost all professional projects I can see that they do not make a mainwindow.ui (I mean: they do not create forms for them), but make ui for another less important windows. It could be configuration windows and so on.
The questions is Why?, Why don't do a mainwindows.ui and create this one by code?.
There really isn't an "answer" to that question, it comes down mostly to the preference of the programmer and the way they are used to do things. One reason may be that many projects will use QMainWindow instead of creating the main window (along with menus, tool-bars, status-bars, etc) by hand.
In the end, it's up to you as the software designer to decide which method is most appropriate/preferable in the context of what you're making.