If one uses one of the four HW shortcut versions to uncompress an odf as indicated in an older post, does it do so only within the selected HW instance, or is it done globally?
It is stored separately for each configuration, however the resulting ODFs are stored in a single folder (either the CustomOrganDefinitions folder or the OrganDefnitions folder) so each time you load the same organ but change the setting in a different configuration it will change the ODF. For simplicity I would just leave the auto-compacting turned of while working on files, it just makes things simpler all around. It may take slightly longer to load the file, but being that you're working on creating files in the long run I feel it's quicker to do this rather than go back and forth between compacting and un-compacting the files.
Auto-compacting for organ configuration settings are stored separately for each instance, but the combination sets will share the same folders (similar to the ODFs). However you shouldn't need to be editing these files directly anyway, so just leave them left to auto-compacting.
Does this decompression reveal all the CODM tables, used or unused?
It will show all tables that were originally included in the ODF.
Finally, but somewhat unrelated, is it simpler to strip out un-needed features from a CODM, or cut and paste needed items to a new CODM?
That is up to you really. At first I would suggest removing unneeded options from an existing CODM file (one at a time) and modifying the rest to suit. Then once you become more familiar you can always try cutting and pasting the items you need into a new CODM file.