I've never worked with
Email::Simple::Markdown, but the doc says you feed it with
Markdown and it creates a multi-part email with the original text and the generated HTML version.
From your previous description mentioning templates it seems you fed it with HTML right away, which could explain all your problems.
Probably you just want to use Email::Simple ?
update
NB: please note also that lines longer than 78 characters (80 with CR LF) are discouraged by the RFC. (>998 are forbidden)
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