heh, it’s already fixed in Chroma upstream 
Now Chroma supports the original Pygments class names. So the CSS files used for Pygments can be used for Chroma too, without any modification.
Why does standalone chroma do better highlighting?
That issue was present in the Chroma released with Hugo 0.29, which also was fixed later. It is this issue. Chroma was lacking parsing of Emacs Lisp keywords. Alec Thomas, Chroma developer, was kind enough to quickly add that support.
See if this helps you; it’s a bash script to build using master branch of Hugo with master branch of Chroma. If you use 64-bit Linux, you can use the binary I built using that script.