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I understand and appreciate the intent the problem, but you want to have control over which companies are used by an organization. Yes they are shared at the set level, but you may not want them to be automatically shared to the org(s). It's like with item, they too exist at set level, but you have to deliberately share them to the site...and thus the org.
It has never made sense to me why they would structure Item Sets in one way and Company Sets in another. There should not be a "Master Company" record. If a Vendor is shared across Organizations in a given Company Set, there should only be one record defining that Vendor, not one for each Organization that can potentially have different Names. While some information (e.g. - GLs) might need to differ by Org, that should be handled similar to the ItemOrgInfo.
Since my clients have all had a single Organization, we have been able to work around the issue by checking the "Automatically Add Companies to Company Master?" checkbox for the Company Set record in the Sets application which allows us to ignore the existence of the "Master Companies" application.