I don't think there is an easy fix here.
PreTeXt produces something like this:
\begin{equation}
-K\left[\frac{T_x(x+\Delta x, \, y) - T_x(x,y)}{\Delta x}\right] \Delta
x \Delta y \approx -KT_{xx}(x,y) \Delta x \Delta y \tag{2}
\end{equation}
When \tag{X} is present, MathJax adds margin to either side of the equation based on its calculations of the size of the number produced by that.
So say the equation is 500 pixels and MathJax decides that the number (10.5.4) takes 60 pixels. It renders a 620px wide box for the equation. There is "dead" space on the left because it is trying to make sure there is space for the number on the right but the equation itself remains centered.
If what MathJax produces is too wide, none of our options are great:
* Current behavior - overflow
* Cut off the right side and make it scroll
There is not going to be a reliable way to override the spacing MathJax produces internally.
Other options:
* Rewrite the source so that equation takes up less space.
* Force a smaller font size for the math.
* Rewrite the math logic so it does not insert the number as a tag in the text MathJax will process. Instead, set up something like side by side divs, one with the equation and one with a number. Then try to write layout code that keeps the numbers lined up and forces just the equation box to scroll.
Andrew