I think that is a frequently asked question about the behavior of figures in beamer slides produced from Pandoc and markdown. The real problem is, R Markdown produces PNG images by default (from knitr), and it is hard to get the size of PNG images correct in LaTeX by default (I do not know why). It is fairly easy, however, to get the size of PDF images correct. One solution is to reset the default graphical device to PDF in your first chunk:
```{r setup, include=FALSE}
knitr::opts_chunk$set(dev = 'pdf')
```
Then all the images will be written as PDF files, and LaTeX will be happy.
Your second problem is you are mixing up the HTML units with LaTeX units in out.width / out.height. LaTeX and HTML are very different technologies. You should not expect \maxwidth to work in HTML, or 200px in LaTeX. Especially when you want to convert Markdown to LaTeX, you’d better not set out.width / out.height (use fig.width / fig.height and let LaTeX use the original size).