It is most likely not possible.
First, the original Markdown rules state:
HTML is a publishing format; Markdown is a writing format. Thus, Markdown’s formatting syntax only addresses issues that can be conveyed in plain text.
That being the case, things like left-aligning text is outside the scope of Markdown. Of course, the appropriate way to do that is to use raw HTML, as you have tried. But that's were you run into problems with Pandoc.
Pandoc's documentation states (emphasis added):
Because pandoc’s intermediate representation of a document is less expressive than many of the formats it converts between, one should not expect perfect conversions between every format and every other. Pandoc attempts to preserve the structural elements of a document, but not formatting details such as margin size. And some document elements, such as complex tables, may not fit into pandoc’s simple document model. While conversions from pandoc’s Markdown to all formats aspire to be perfect, conversions from formats more expressive than pandoc’s Markdown can be expected to be lossy.
As left-aligning text is not something you can do in plain Markdown, then it is the sort of thing you can expect to get lost when converting to other formats. The reason it works when converting to HTML is that the raw HTML is simply passed through unaltered. Standard Markdown behavior it to not even parse the HTML. As the output is HTML this works. However, when using Pandoc to convert from Markdown to non-HTML formats, the "formatting details" in the raw HTML is lost.
Sometimes you can successful convert from an HTML document to another format with a little more success, but the supported features outside of Markdown are severely limited. From time to time I have seen people even attempt to create the Word document they want, then use Pandoc to convert that to HTML to see what Pandoc produces. Even then, in most cases the formatting is lost as it is not something that can be conveyed in plain Markdown.
