Hello,
Math equations have some limitations related to alignments. We recommend you to use DOCXCustomizer (https://www.phpdocx.com/documentation/introduction/docxcustomizer) to change alignments on the fly if needed, maybe you need to set both w:p/w:tc and math alignments.
If you open a support ticket (https://www.phpdocx.com/support) with your template and the smallest code inserting a math equation, the dev team will generate a custom script to illustrate how to accomplish it.
Regards.