That is strange that the code chunks don't have a clear Style associated with them. When I knit the standard R Markdown template to Word, every section is associated with a style except the code chunk and the output.
A short-term solution would be to experiment with the highlight argument. From ?word_document:
Syntax highlighting style. Supported styles include "default", "tango", "pygments", "kate", "monochrome", "espresso", "zenburn", and "haddock". Pass NULL to prevent syntax highlighting.
For example, you can remove the grey background and other colors by setting this to NULL in the YAML header:
output:
word_document:
highlight: NULL
Unfortunately that still doesn't make the font of the code chunk match that of the Body Text style.
A potential solution, albeit convoluted, would be to use a knitr hook to add fenced_divs around the code chunk and then define custom styles in the reference docx file.