The short answer is "yes you can".
However in order to answer your question to why modules are unavailable, could you please share some additional information regarding the code?
I wanted to add our social media icons to the footer of the email, so I copied the variable definitions at the top from a different template that already has that footer into the new template. Then I added the table to the bottom of the HTML. The social media icon footer looks good in the email, but once it was added, the module section on the right was no longer available.