Is it possible to make the links in this newsletter blast contain the Munchkin tracking code, even if the email is not being sent from Marketo?
No. But the immediate reason is that Munchkin isn't involved in Clicked Linked in Email activities. Click tracking works by rewriting links to bounce off the Marketo click tracking server (the "branding domain"). Munchkin only loads on the webpage visit that immediately follows the click. Even if the target site doesn't load Munchkin at all -- or if the browser doesn't support JS -- you still log the click activity.
So what you're really asking about is click tracking code. I feel like someone else asked this recently... and the answer is no, you can't fake or extract the links that Marketo itself would generate for a given email. Those links encode both the Marketo lead and information about the send and individual link, and you need to use Marketo to take advantage of them.
That being said, if your 3rd party partner can embed the email address itself in the clickable links, then you can use that information in the same way that you would if someone went to your site and filled out a form. Some people find it unprofessional to show the email address in plain text in a URL, so you could ask them to Base64-encode it first (so it will look like "random" letters and numbers to most humans but in fact is a standard encoding of the address that you can decode on your server to associate the web activity with a lead).
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