I think that the migrations_script_directory config and the related executeScript(Database $db, $file) method add little value for the extra overhead.

https://github.com/doesntmattr/mongodb-migrations/blob/master/src/AntiMattr/MongoDB/Migrations/Version.php#L261

It would be easy enough for anyone to load the javascript file and run it directly against $db in their own migration if they wanted it.

I would like to make this feature deprecated to be removed in 3.0.