Equations in EPUB created with Bookdown are not displayed on a Kindle ebook reader

If you inspect bookdown::epubbook you can see that it already adds --mathml which overwrites your --webtex argument passed to pandoc. That's why it does not work. bookdown::epubbook already uses --mathml for converting TeX:

See this https://pandoc.org/MANUAL.html#math-rendering-in-html

The docs even state, that mathml only works for select epub-readers. So giving your argument does not change anything because it's overwritten by --mathml.

> format  format$pandoc$args
 [1] "--metadata-file"                                                         
 [2] "C:\\Users\\..."    
 [3] "--webtex"                                                                
 [4] "--number-sections"                                                       
 [5] "--toc-depth"                                                             
 [6] "2"                                                                       
 [7] "--mathml"