For SmartGit 17.1 there is a work-around: the Log contains the "Rebase Interactive From" command in the immediate history of the current branch. You can use this to change the commit messages, too.

Or behind the Amend-checkbox a combobox with the amendable commits could be shown...

I think, this is not possible with reasonable effort because a simple is-different-comparison is much simpler than creating a diff for each file (counting the minimum number of changes).

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.