The GUI is actually not expected to change.

That's true. The option will just execute the system Git-Flow command instead of SmartGit's built-in Git-Flow. So your request makes perfect sense.

In the Preferences, section Executables, you can select Use pre-installed ("system") Git-Flow.

Sounds like a generalization of topic http://smartgit.userecho.com/topics/419. We most likely won't implement concurrent Git operations, because of all the possible problems when accessing a complex database (like Git) concurrently.

This sounds like a bug. Does "git status" show proper results?

Are you looking for some kind of automatic Reveal Commit? I guess this can become confusing if the graph constantly changes when you are changing selection (or just stepping through Branches view, using keyboard). Also, this can become really expensive when the selected branch is not yet visible.

You can use Ctrl-A to select all, then toggle all of them at once using Space key.

Please give more details what you actually mean: what should be selected/deselected? Under which conditions?

Have a look at: https://groups.google.com/d/msg/smartgit/wOIZ0Thli8k/_JFAjQtqAwAJ

Maybe you are just looking for https://smartgit.userecho.com/topics/27?