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Good day Adam Monago - good question!
In my experience there is a very specific field to denote the primary contact related to an Opportunity for Marketo to see the relationship. That field is the customerid field in MSD on the Opportunity, a standard field. If you use a custom lookup field Marketo doesn't know that that field's purpose is to connect the Contact and the Opportunity.
Please let me know if you have resolved this, or if I can help you further on this!
Our CRM Dynamics team ask me to list things that I would like to sync between Marketo and CRM, Do you have any pre-built concept template I can refer to?
Suzy from SoftwareONE
Thanks Paul for the reply. For whatever reason I only encountered it now, but it is useful.