To be clear, LaTeX is not involved when the output format is Microsoft Word. Instead, Pandoc is converting the math into Office Math Markup (OMML), part of the Office Open XML standard.
This is understandably confusing
since the R Markdown source uses LaTeX-style markup for the math, but that’s basically just a convenience (since LaTeX-style math markup is perhaps most familiar to end-users).
But yes, Preview does not display all aspects of docx files with perfect fidelity, and OMML is one of those cases. It’s a good idea to check the document for rendering errors in Microsoft Word itself
.