Edit MSI to allow use of a custom synced field

We are currently looking to implement MSI in a synced ENV to reduce the necessity of multiple Marketo instances. We have hit a limitation that where the GUIDs match between the 2 ENV's MSI works correctly, but where the GUIDs do not match, it cannot link the record between D365 and Marketo. We do have a synced custom field (synced between D365 ENVs and Marketo) that could be used as a unique identifier between all 3 ENV's.