Your comments

What exact Git commands Tower is using?

Solve in 20.1 preview if the option "Follow only first parent" is selected.

SmartGit has an option "Pull: prune obsolete remote tracked branches" in the repository settings since a long time. What further option do you need?

Of course, SmartGit has this feature: Local | Run Garbage Collector - but it is completely unrelated to this request.

Unfortunately, I have no idea how to change the repository settings easily for multiple repositories with possible contradicting options. Maybe the simplest solution for you would be to add an external tool in SmartGit that configures the user.email option according to your needs, e.g. execute the command

Command  : {git}
Arguments: config user.email user@domain.com

Then setting it is just one click in the Tools menu.

That is very easy to achieve. Open the Open Source repository in SmartGit, use Repository | Settings and enter the different email address. This will write the user.email to the repository's .git/config.

What exactly needs to be different for your open source projects than for the others - email address?