How to access custom object with intermediary object.

For anyone looking for more details on the setup in the question:

• In your Salesforce Object Sync, you would enable sync on the "Courses" object. Leave "Course Registrations" grayed out. Those Course Registration objects will come over because of "Sync Implied".
• Wait until all the Course objects come through in the sync. It'll take a while. You can see the object count in Marketo Vs. SFDC object count when you click on the details of the object
• Remember that the mapping between Leads->Course Registrations->Courses is done through a lookup kind of field. Which means that the Lead needs to have been updated/modified in order for Marketo to pull in the related connection to Courses. So each time you add a course, make sure to also update the Lead in some way.
  
  

And, if you are here because you're looking for a way to have Leads + Contacts point to multiple objects through an intermediary object, here is an example of something I tested.

Here is our setup. There is a Many-to-many mapping that can happen between Leads, Accounts and "Tenant" objects. This is done through an intermediary "Tenant Mapping" object. To complicate things, the Lead and Account could point directly to a Tenant, not going through an intermediary object (but I didn't care about that scenario for Marketo setup purposes).

This is what the Salesforce Object Sync map looks like when you refresh the schema. You can see that, under the Lead, there is a "Tenant" listed directly (this is for getting the tenant that's directly linked to the Lead), and there is a "Tenant Mapping" with a "Tenant - Lead" underneath. That's the one we want to sync over - because it uses the many-to-many intermediate object. Note that "Tenant - Lead" and "Tenant - Account" originally came through as just "Tenant". You have to rename them so they're unique. Marketo will pull the data only once (it won't create copies of the Tenant rows) - this is just a cosmetic renaming you need to do.

Sync only the objects in green. Marketo will "implied sync" the intermediate object.

Detailed view. You can see how many of the Tenant objects are available in SFDC, vs. how many were brought over to Marketo. If you refresh this window during initial sync, you'll see the Marketo go up on each refresh.

The result:

• For people who are SFDC Leads, Marketo is aware of all the Tenant objects connected to them.
• For Contacts, Marketo will look into the Tenants associated with the Account they belong to. That means all the Contacts under an Account will be aware of all the Tenants that the Account is connected to. 
• Again, because the linkage between Lead->Tenant and Account->Tenant is a lookup field, Marketo won't update the Tenant data until the Lead or the Account is updated. Each time you alter/add a Tenant / Tenant Mapping record, you have to update the associated Lead/Account.
• Because the Tenant objects have different names and are seen as different filter conditions, your filters have to check both: in case the Marketo Person is a SFDC Lead or a SFDC Contact

Huge thanks to Veronica Holmes who explained a lot of this in the following video: https://www.youtube.com/watch?v=qXt1CPMZReA 

You can't access 2nd-level objects from Velocity, so no, this isn't the right structure.

If you search past threads for "second level objects" or other variations, you'll see this discussed at length.