What if multiple repositories are open in one SmartGit window?

The next 17.1 build will have a toolbar button for the base file changes.

SmartGit already creates an empty commit when initializing a new Git repository.

What would be your benefit except of having to download less?

Have you tried 17.1 RC 1? There the Pull toolbar button has a popup menu (click and hold) containing the dialog-less Fetch command.

We consider to implement something like that in the near to mid future.

Could you please describe in more details why you want to customize the work-flow, what you don't like about the current (default) work-flows?

At the moment this is a technical limitation.