I think there is still several approach.
have pandoc convert to your markdown flavor
It just supposition but you can also create custom output in PANDOC using LUA filters
Pandoc has a modular design: it consists of a set of readers, which parse text in a given format and produce a native representation of the document (an abstract syntax tree or AST), and a set of writers, which convert this native representation into a target format. Thus, adding an input or output format requires only adding a reader or writer. Users can also run custom pandoc filters to modify the intermediate AST.
See also custom writers.
Also check that pandoc does not already support your flavor through its variants and different options.
If you manage to do that, with the right configuration you could use rmarkdown and build a custom output format.
knit to your flavor
I think this would be possible, but I am not sure knitr exports all the tool required for that. It won't be documented, and you need to read the code.
Note sure what is the best way to tackle. It is no so clear what it involves when dealing with specific flavoir.