POD has you covered. From perldoc perlpod
For, begin, and end will let you have regions of text/code/data
that are not generally interpreted as normal POD text, but are
passed directly to particular formatters, or are otherwise special.
A formatter that can use that format will use the region, otherwise
it will be completely ignored.
So you could write a Markdown POD formatter that would look for these and interpret the paragraphs as Markdown.
The following are good parameters:
Since the text is otherwise ignored if the formatter doesn't know how to handle it, you don't get weird-looking stuff in your output if this runs through the usual POD formatter.