Is there a way to unsubscribe the same email address on one brand while shared on a separate brand?

That's the Durable Unsubscribe functionality kicking in! It basically is an OOTB system functionality that ensures that a person who has unsubscribed from your email will not be re-subscribed without them re-subscribing again. Marketo maintains a master email status record for each person, which is separate from the Unsubscribe field visible on the person detail record. When the Unsubscribed field is set from false to true, the master email status is updated, and the change is propagated to other leads or contacts with the same email address. This means that even if a person is removed and recreated, or if a new record is created with the same email address, the unsubscribe field will not be overwritten.

You can always create custom Unsubscribe fields for maintaining preferences individually for each BU/product category. You can still use the system Unsubscribed field as the master Unsubscribe field, and having that field set to True would Unsubscribe people from all BU's marketing emails (equivalent to unsubscribing from all marketing communications). You'd need a solid preference center campaign setup to ensure everything is in order and in line.

This is Marketo’s Durable Unsubscribe feature. You can’t turn it off, but you can react to (that is, trigger on) the automatic push of the the Unsubscribed value to other people and use custom fields instead.

However, be very careful that you are not going against the wishes of the end user and that they unsubscribed in a brand-specific context. You must still allow people to say “none of your subsidiaries may contact me.”