Pandoc is great!

...except if you want to batch convert real-world markdown.

Though admittedly, that's mostly because markdown designers thought allowing embedding of arbitrary HTML was a good idea.

(The best you can get is by going: markdown -> HTML -> $target_markup.)

The ability to embed arbitrary HTML is an intentional feature of Markdown.

aepiepaey agrees with you that it's an intentional design decision ("thought ... was a good idea"), and his/her use of past tense also implies that s/he disagrees with the decision.