Why isn't the setting for project folder mapping included in the Project Editor?
Please move it there.
And if you really want to implement it so that it's easy to configure, make a column of check boxes that can be used to turn the mapping on or off for each entry in the project file that involves a path.
Checked box = mapping on
Uncheck box = mapping off
And while you're at, please make the feature so that it downloads ONLY the files that have been changed instead of all the mapped files. Kind of like how an incremental backup works.