Marketo and Salesforce Unique ID as Email Address

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By default, the unique identifier is the SFDC ID...

That’s not accurate. In Marketo, the unique identifier is the Marketo Lead ID. Multiple SFDC IDs, or no SFDC ID at all, can relate to a single Marketo Lead ID over time.

In any case, there isn’t a way to change how records are matched from SFDC the first time... because there isn’t actually a matching step at all. New records created in SFDC create new records in Marketo.

If you want to check new people after they’re created in Marketo to see if there’s another Marketo-only person with the same Email Address, use a webhook-compatible service. That service can also merge people automatically using the REST API. (If you want to auto-merge people, you need conflict resolution rules for all fields or else you can get a mashup of values from each person.)

Alternately you can do a 100% sync so the people will be in SFDC from the start.

Well, Marketo doesn't De-duplicate people getting created from Salesforce. Also, SFDC Id should be unique for all the records in Salesforce (similar to the Marketo Lead Id). Also, you can have multiple records with the same email addresson both platforms, so you’d still face duplicate issues. You should look at finding the source of duplicate records on both platforms and try to eliminate those. You can also set up what's called a "Conditional Sync" if you want to disallow certain records (duplicate records in Salesforce) from syncing back to Marketo. This entails creating a boolean/checkbox field in Salesforce (and then allowing it to Sync) and then contacting Marketo Support with a request to set up Conditional Sync using that field.