Hi Jorge -
For the time being, we're only allowing text-based email templates, though will explore HTML email templates in the future which would give you greater control over how links are rendered. I'll include this item in our internal prioritization discussion, though we will not likely make any changes in the short term.
One other recommendation that I would make is to look into the mail clients most commonly used by your users and see if there is a way in which they'll pick up the custom scheme from a text template, though that is likely to only provide partial support.