The templates that you download from templates.marketo.com often have them in place already. It will work with a system token (glossary here: https://community.marketo.com/MarketoArticle?id=kA050000000LBvaCAG). If you are using a program token (my.token) then you need to make sure every program you use the email template in has the my.token already created in it.
At the summit, one of the Champions showed you can ensure this through creating the token on a folder that houses your email programs. Creates a token hierarchy or something. Not sure of the terminology but I was just testing it and it seemed to work. They may post the video or pp deck.
The link you provided is a dead link. I searched for system token on the community and they only list off:
Sorry I had a bracket on the end of the other link.
I would just create a folder called Universal and stick all your other folders and programs under that. Create the my.token on that folder and it should roll down to all your new programs.
Thank you Jamie for your help.
Also, try out using Rich Text tokens. You can edit the body copy of various sales emails via the Tokens tab.