This is great that this now works but a really bad implementation. Because now logic has to spread all over the place. I can't just create a token for the url, its really a token for the whole HTML including the <a> tag.
We have created an Email Template using Email Editor 2.0.
The links are being defined using variables:
<meta class="mktoString" id="c1ctaURL" mktoname="C1 - CTA URL" mktomodulescope="true" default="#" />
We applied the workaround mentioned in a few posts above in order to get these links tracked:
Doesn't sound like this is related to a user-authored Email Script token, so should be a new thread.