For anybody lurking, I worked with Marc via screenshare and we figured it out. It isn't actually a discrepancy with his instance or anything that hasn't been documented (albeit implicitly) before.
The person who wrote Marc's template didn't understand that the variable CTA-1 URL, when set to grab the output from {{my.Script Token}}, isn't just a URL. It's an entire <a> link including the closing </a> (as always required by Velocity). And you can't put an <a> inside another <a>, that's broken HTML.
Therefore the solution is to output the equivalent of CTA-1 Text and CTA-1 URL from Velocity, and remove those variables from the template.
.png)