One option instead of using the Auto-Assignment (Lead Assignment) rules in SFDC is to assign new records to a SFDC Queue.
In Marketo you won't be able to send alerts to a queue. You also won't be able to select the Leads owned by a specific queue in a Smart List. In Marketo if the SFDC Type = Lead and the Lead Owner fields are blank, the SFDC Lead is owned by a queue but you won't be able to determine by which queue. There is no out of the box way to create a list of leads owned by a specific queue, you would need to do something like create a custom field in SFDC and copy the queue name to the field.
If a SFDC Contact runs through the Sync Lead to SFDC flow step, since Salesforce does not allow "Contacts" to be assigned to lead queues, Marketo will create a duplicate "Lead" in Salesforce. If you want to prevent this behavior in your campaigns, adjust your smart list to only allow Marketo only records flow through the smart campaign. Another option is to use Add Choice and prevent SFDC Contacts from flowing through the flow step.
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