I wrote my dissertation in markdown because LaTeX added so much noise to the text. In the end I had to go back and manually reformat chunks of it in LaTeX (especially the floats), but it was still worth it for all the bits I never had to write LaTeX for. In the end, it's not either-or, it's Markdown plus conversion to something with more knobs to turn. (All thanks to Pandoc!)
Pandoc even lets you include LaTeX in your markdown, so you can just use it inline for the few times you need more control, without having to faff around editing the output.
Yes. Depending on what are you including, a better alternative might be to use Pandoc filters that change their output depending on the output format. So for latex you might end up with fancy figures side-by-side, but for word you just have them as figures one after an other
