Currently, any links present in email script token are not automatically tracked. My idea is to provide the ability for links to be replace with tracking links if they are present in the html of the email script token.
An easy way to do this might be to provide a Marketo "tool" in the Velocity Scripting platform (similar to other tool objects that Marketo provides).
So, for example, you could have a velocity scripting method like $marketo.makeTrackingLink(String URL) that would take in a URL and convert it to a marketing click-tracking link.
That way, email script writers could just use this method to make their links trackable when they are inserted into their email and there would be no need for Marketo to re-scan the email for tracking links once the script is executed.
Opened a support case on it. They are not tracked if the anchor text is a my.token. I'm sending people to a specific page on the site using a url with a my.token slug and displaying the name of their page with a second my.token as the anchor text. Marketo says no cigar and had no alternative method. So I don't track it.
That doesn't have to do with email script tracking. Non-Velocity {{my.tokens}} aren't available in Velocity. When Velocity outputs a fully-formed <a> tag it is tracked -- I've written extensively about the details.
You could, in fact, move your {{my.tokens}} into Velocity tokens (as variables) and have another Velocity token output a tracked <a>.