We currently use one Short Code within SFMC, and are bringing on two more short codes for different programs/brands. If one short code customer uses a global 'STOP' keyword, does this affect outbound SMS to other short codes where the customer is using the same mobile number but subscribed to multiple program short codes? SFMC documentation suggests that the _SMSMessageTracking is tracked at the Short Code level, but the fields on the _SMSSubscriptionLog table does't have a field for short code. How are custom keyword opt-in and custom keyword opt-out tracked in SFMC?
Each "global" stop can only be related to one shortcode, ie the one it was used on. The "global" stop allows one message to opt them out of everything on that shortcode. The global stop for Shortcode #1, can only unsub for shortcode #1. It is "global" in relation to that specific shortcode and all the keywords you have associated with it. Think of it more as a Parent keyword that overrides all the other keywords on that shortcode.
While you may have multiple shortcodes set up in MobileStudio. SFMC treats them as separate entities. If you wanted a keyword to opt them out of all the shortcodes you would have to build an automated process to unsubscribe them from any other shortcodes.