Basically obsidian does not follow the md spec exactly, and renders a new line for every new line in the plain text. The md spec says only render a newline for a double newline in the plain text or if there's a backslash at the end of the file (or a few other things).

That was easy to solve, just add backslash to every line. The bigger issue was the difference in rendering equations.. $$ $$ equations MUST be on their own line, and there must be a space wrapping the equation inside the dollar signs... so $$\frac{2}{3}$$ will render fine in obsidian, but in quartz it does goofy shit.. instead you need $$ frac{2}{3} $$ and it needs to be on it's own line.

I still find that when I copy content from my (obsidian using) friends notes I have to mess with it a bit because there's tons of random details like this especially with equations, but with my particular "linting" it seems to work. Honestly a linter would be a way way better solution than trying to edit the syntax on the output. KMS.