It is possible to supply batch commands directly with the -b flag, but if the commands become very long, this is no longer an option. Is there a way to give the path to an .scm script that was written to a file, without having to move the file into the scripts directory?
No as far as I know. What you give in the -b flag is a Scheme statement, which implies your function has already been loaded by the script executor process. You can of course add more directories that are searched for scripts using Edit>Preferences>Folders>Scripts.
If you write your script in Python the problem is a bit different since you can alter the Python path before loading the script code but the command line remains a bit long.