When you use {{system.unsubscribeLink}} the unsubscribe page's link will be placed in the email, but it will never be converted to a shortened tracking link. It will still work for the user clicking it, as it has the mkt_tok parameter appended to it. If you don't use the {{system.unsubscribeLink}} token, then Marketo will automatically place the unsbuscribe info (whatever you've specified in your Admin section) at the end of your email and it WILL be in the form of a shortened tracking link. This is not related to Email 2.0, it has always functioned this way.
Whenever you have a complete URL encapsulated inside of a token, Marketo cannot convert it to a tracked link. Try it yourself, put http://www.example.com inside of Text my.token. If you use that as the href of one of your links, it will be placed in the email, but NOT converted to a tracking link. And you will see the same behavior you're describing on the text version of your email. Note that it will be tracked if you make the token www.example.com and then specify the href of your link as http://{{my.token}}
Now, we should probably remove excess [[ ]] characters from the text version if we were unable to convert what was there to a tracking link, but that would just be a small improvement to this behavior. I would recommend you just remove the [[ ]] characters if you plan to use the {{system.unsubscribeLink}} token.
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