When you insert a single line break in the editor, it creates a single line break within the current paragraph. Two new lines are required for a new paragraph, which is why the last line in these examples ends up bundled with the quote. Pretty sure this is by design in Markdown.
However, I think I can mitigate it by inserting an empty bracket at the end of the quoted post in the reply form. That way, even if this happens…
> Quoted text.
>
Reply here.
…it’ll work.