I would like to specify which files do not auto-unsync. I looked at your CLI commands, but do not see how to make that happen.
Is there a way to make this happen for individual files? If not, can at you least make all files inside a folder not auto-unsync? This solution is more cumbersome, but at least would handle the challenge.
With the CLI and some scripting it is possible to run your own auto-unsync loops, excluding or including the paths that you want. This would not make use of the built-in auto-unsync functionality, but would give you a lot more control.