Can confirm Costco Addendum findings are subtracted from your total SQF score. By applying the Costco Addendum to your scope, it effectively becomes part of the code you are being audited against. The logic makes sense to me: you run your normal operations and everything goes okay, but when the auditor wants to observe a process related to Costco they witness a critical finding, they're not just going to fail your Costco portion. Most of the plants I've worked with have regular customer product running via the same lines and processes as the Costco product, so counting them separate for audit purposes isn't representative of the work you're doing.
Additionally, Costco Addendum isn't a full code in of itself. It relies on the base program elements of SQF code, only calling out more stringent requirements on areas Costco believed SQF was too lax for their standards.