What should be the result of having pinned them?

A workaround for the meantime could be to use 2 instances of SmartGit (using the portable bundle), one for the Windows repositories, one for the WSL repositories.

The problem is that SmartGit not just executes a few Git commands (like other Git clients do) and parses the output, but instead directly accesses the file system to read the files and especially the .git directory content, watching for file changes. Tunnelling this through SSH would mean to split a major part of SmartGit into 2 parts - not impossible, but a lot of effort. I reckon, not much users actually would want to have this feature if it would cost x00 USD extra.

This would mean to rewrite SmartGit from ground. Unlikely to happen.

Do you mean SmartGit should operate on the remote working copy or should SmartGit only be able to pull there all locally committed/pushed commits from the central repository? The first would mean to rewrite SmartGit from the ground.

IMHO this is the task of a good IDE. As you can see, your editor is not smart enough because the args.Length shouldn't be highlighted.

For those who are not using VSCode and its remote extension, could you please describe exactly what you expect SmartGit to do?

We won't implement a modal dialog on a selection change because we consider this very bad user interface design.