Preference Center & Duplicates - Conundrum

I have a conundrum with my opt out.  First off, our organization has intentional duplicates. Not ideal but this is the way our implementation partner set us up, so we have custom deduplication rules in Marketo that looks at email and "company". We have multiple companies in our instance of Marketo. So there can be a scenario where two companies have the same lead (email) but we consider them unique.  

joe@joesauto.com && Company X

joe@joesauto.com && Company y

^^both considered unique in our instance

Our issue is we want to send emails to all the companies in our database so we created a preference center for each company.  If a joe@joesauto.com from company x opts out of company y, then they get opted out on the record for company x.  The challenge we are having is we may get a new list that puts joe@joesauto.com back into our data base as net new for company y.  So now company x and company y have a record in marketo. Company x has the opt out data for company y. 

Here is what I think I need to solve this issue:

1. Ability to identify that an email is a duplicate
2. Ability to identify that one of those duplicates filled out a opt out form 
3. Ability to run a data update that marks the non-opted out duplicate as opted out if 1 and 2 are true

I thought I could use the special filter "Duplicate Fields" to run a data update on all duplicate where Email Address is duplicate then look at those that are duplicates where one has filled out a opt out form for company y, then run a data update on those records. But there are limitations on using advance logic on "Duplicate Fields" filter.

Anyone have any suggestions?