Peter is correct, what you are seeing is the initial fast preview, and then the final typeset version (which uses different fonts). MathJax tries to match the size of its output so that an "x" in the math is the same height as an "x" in the surrounding text. That is the source of the font-size at 121% that you are seeing. I do NOT recommend setting the CSS for .mjx-chtml as you have done; rather you should configure MathJax to turn off the font matching, if that is what you want (though that may make in-line math not line up well with surrounding text). To do that, use
MathJax.Hub.Config({
CommonHTML: {matchFontHeight: false},
"HTML-CSS": {matchFontHeight: false},
SVG: {matchFontHeight: false}
});
Remember that font display differs from browser to browser and system to system, so what you see may not be the same as what others see, so tweaking the output to work for you may end up distorting it for others. I recommend leaving the font matching on, but, of course, you can do what you think best.
Davide