The font metrics in MathJax are given in em units to 3 decimal places. Most characters are about .5em wide, that means the resolution is about 1/500 of the width of the character, so if you enlarge the character by too large an amount, the round-off for that resolution can become significant. You are seeing the results of that limited resolution in the bounding box information.
If you are in a situation where you can use CSS, then you should be able to use
svg {
overflow: visible;
}
(or add overflow:visible to the style attribute on the svg element) in order to see the full character even if the viewBox is slightly too small.
Davide