I think you might be under a mistaken assumption here, because I don't think that this is factual.
The only way I could see your misunderstanding is if you think the quantity of whitespace in markdown tables is important, which it isn't.
This is a working md table and it's not harder to make then the equivalent html version
|Header one|header two|
|---|---|
|Column value 1|column value one|
|value 2|value two|
EtcWherever what's preferable is another story though.
Personally I dislike writing plain html, and would always prefer another template language to generate it, but that's just preference.