The CSS class was being used to suppress the phone link in non-mobile clients through a media query. Thus the display:none in the link. There is a second non-link phone # displayed for non-mobile.
What I think is happening is the clients I am testing with (Gmail and Yahoo Mail mobile apps) don't support the tel: protocol and the link conversion to the Branded Domain url is enabling the link since it redirects to a webpage. So natively it won't work on these clients. Other mobile clients such as Samsung Mail it works. To make things even more confusing, if I remove the tel: link and leave as just text. The Yahoo Mail app converts the text phone number to a link that does work correctly.
The CSS class was being used to suppress the phone link in non-mobile clients through a media query. Thus the display:none in the link.
Then that would explain why you didn't see the link when you removed the special CSS class that happened to control the display: style in your email. But it doesn't have to do with the rendering of the href itself. I was asking you to remove that class to ensure that Marketo sees its mktNoTrack first. (Note that the DOM parser used on the back end is not as sophisticated as a modern browser parser.)
There's only one link sent from Marketo. So even if a browser/device combo doesnt support tel: they will still have the same link, it won't change to an http: tracked link on the fly on the browser side.
Bottom line, the mktNoTrack CSS class changes -- or should be changing -- the link to an untracked link for all recipients.
Here's another way to create an untracked link: put the entire URL (including tel: protocol) in a Text {{my.token}}.