If you use Record Types in SFDC, you can set the Record Type ID in Marketo. Set the value before using the “Sync Lead to SFDC” flow step. Insert the 18-character ID, not the name of the Record Type.
Work with your SFDC Admin to get the Record Types IDs and to determine the logic for which records should get which IDs. Since the Record Type is a lookup field it will contain an ID instead of a name. Here is an interesting article about viewing the name.