Such issue tend to be browser-specific, but you have not indicated the browser or OS that you are using, so it is difficult to duplicate the result.
The configuration that you took from issue #2466 was for version 3.0.5, but you re using the generic version 3, so should be getting 3.2.2. Note that the code is within an if-then statement that only runs if you are using version 3.0.5, so the configuration would do nothing in your case. Furthermore, it is a fix for the SVG output, but you are using CHTML output, so it probably would have crashed in any case (since the SVG output jax is not loaded in your page).
Switching from tex-mml-chtml to tex-chtml would not change the output, since both use the same CommonHTML output jax.
You say that you don't care for the SVG output because "it messes with the CSS", but it is not clear what you mean by that, and that you "have other CSS that affects Mathjax", but don't say in what way. Perhaps it could be made to work with SVG.
Finally, as you have found out, these issues are often sensitive top the font-size and zoom level of the browser. You note that at 20px it works, but at 30px it doesn't. Perhaps 29px or 31px would work, and that would be sufficient for you?
In any case, the next release will include an update to the fonts, and I'm hoping that will resolve the issues like this.
Davide