Hello,
We have dome some tests. The MathML to the Word format is done through a XSL file, so you need to use the correct input; for example instead of mi tags, use mn ones.
Phpdocx replaces automatically these tags, but only if they don't have attributes, so maybe you have removed that lines of the code.
This example works perfectly with MS Office 2013:
$mathML = '
<math xmlns="http://www.w3.org/1998/Math/MathML">
<mrow>
<mn mathvariant="bold-italic">x</mn>
<mn>y</mn>
</mrow>
</math>';
$docx->addMathEquation($mathML, 'mathml');
Regards.