Alexander -
If I understand you correctly, what I think you're saying is that the links you are trying to track are not at all in the email template that you built in the Marketo Design Studio, but actually constructed in an email script token (using Velocity). This token constitutes the entirety of the body of your HTML message to your leads?
I just checked some of my own messages that I built using the same method and can confirm - the links that you construct (and that Marketo delivers) via the email script token are not encoded for tracking. Links in the same message that are *not* constructed using an email script token *do* get encoded for tracking. It appears that Marketo processes links in the *body* of the message for tracking *prior* to interpreting the output of an email script token.
This makes me wonder what happens when you pass just a piece of a link as a token into the body of your message. If the token is generated via an email script, my guess is that it would fail to be encoded and tracked as well.
Bottom line: I think I get what you're trying to do and there's no way, short of Marketo making a product enhancement, for you to both track your links *and* get the sophisticated level of automation and personalization you want. The best you might be able to do is to add your own tracking codes to each link (using source and sub-source URL parameters) and track these on a per-person basis in whatever analytics package you use on your website. At this point, however, any flows you'd like to set up based on click history or advanced reporting that you might try to perform within Marketo are basically dead in the water.
It's increasingly clear to me that there are very few folks (even within Marketo!) who know all the ins and outs of how email script tokens work. It's been a steep and somewhat painful learning curve for me personally. I'd like to see more documentation on using Velocity to create email script tokens. If you (and others reading this discussion) agree, please like the related idea that I posted and add your comments with suggestions on what needs to be documented:
https://community.marketo.com/MarketoIdeaDetail?id=08750000000JYPuAAOThanks,
-patrick