You wrote:
> My goal is to preserve storage, and provide a 'master' copy of these files so they can be updated in one place.
The new (Moodle 2) concept of Repositories was introduced exactly for this reason. There will only be one copy of each unique file, even if different users upload it in different places, with different names! (magic ;)
Note that the File system repository does not fall in to this category. It came later.
> I also have to allow that the course might be restored to a different site, and the file links need to be restored. I'm specifically using File and SCORM resources.
Well, the reverse is not true. If two courses have the same file, it will be in each backup, logically. (Well again, if this is not in the File system repo.) Never tested.
> My first though was that a File system repository would do the job, but that seems to be problematic when restoring courses, including restoring to a different server, or in the event of File System repository change (eg. repository deleted).
I don't know, how references to the files in the File system repository behave during course backups. You have to experiment.
> Should my aim be to get a master copy of a file into the 'Server files', eg. from a File system repository using 'Make a copy of the file'. Then when using the same file elsewhere, select files from there and use 'Create an alias/shortcut to the file'?
Might work, if you use those Server files in your courses. Sounds like a work around for me? You need to understand. The concept of the Repository (as opposed to a directory structure) was invented to make the life of the most basic user pleasant. It bites everybody else!
I wonder whether having the master in a "cloud" and making local copies using 'Make a copy of the file' wouldn't be a better solution.