There seems to be a long tail of formatting tweaks to the emails and I can see differences of opinions on how they should look and what they should contain. ie I'd personally prefer to strip out most of the redundant wrapping and make it streamlined more like github or google doc emails.
But rather than argue about it, why not just move forum_make_mail_text, forum_make_mail_html and similar into a renderer so a theme can override it? Why shouldn't emails be first class citizens
mod_assign_renderer->email_text(...)
mod_assign_renderer->email_html(...)
mod_assign_renderer->email_digest_text(...)
mod_assign_renderer->email_digest_html(...)
Maybe even new layouts to wrap all emails regardless of type across a site
/theme/xyz/layout/htmlemail.php
/theme/xyz/layout/textemail.php