How can I apply logic in user registration welcome emails?
Pretty ugly, but I have a solution. Please post if you have a better one that can be applied for more use cases.

So I installed the https://www.drupal.org/project/computed_field module.

I added a hidden computed filed to my user registration form with my logic.

Then I used the token module to include the value of that computed field in my user welcome email.

It does the job, but again, it is pretty ugly. 
Hopefully this helps someone until someone posts a more direct solution.