Text-only emails are built from text defines located in your language files, whichever language file is used for each page. So a create-account email will use the create-account language file when finding content for email messages. Plus the email_extras language file.
HTML-formatted messages are built from the SAME defines in the language files, and then the content is assembled based on the instructions in the email templates in the /email/ folder. So to make changes to BOTH formats, you would do your changes in the language files directly, since those will be reflected in the HTML version as well. If you're making additions, then you really ought to just add them onto the existing language defines, and NOT create new ones, else you'll need to make many programming changes to incorporate new ones in all the places they belong.
You can change the email "default" preference from text to html in Admin->Configuration->Customer Details. This will affect only future customers, not existing ones.
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