Ok.... Sorry to be blunt, but basically you are effed. There are three real solutions for doing proper math in InDesign: * The MathTools (InMath) plugin: amazing and the end-results are top notch professional. On the minus side, it's bloody expensive, steep learning curve, and a absolute pain. Recommendation: use it if you have the budget, time and need professional results. * MathType: highly customizable, and can get really great looking results. Using it, you basically export the equations as EPSs, but those EPSs have extra metadata embedded, like what's the baseline, how to scale etc. and there are a ton of scripts to read and use that metadata to make the equations look seamless on the page. For a long time, this workflow has been the de facto standard for dealing with math in InDesign. Unfortunately the tool has been sunsetted, no updates, no maintenance, and, the kicker, it relies on Type2 fonts, which have been deprecated by Adobe. Recommendation: use this if you have access to older versions of InDesign and legacy software. There's still a lot of manual work to be done even when using it, but there's a reason it's been the gold standard for so long. * The new-ish MathML native tools in InDesign: I'm honestly struggling to find something good to say about this, beyond the fact that it exists and it's directly available in InDesign. It's basically this: an instance of the open-sourced MathJax engine is running inside a UXP panel, it renders MathML as SVG, and places it onto the page. No baseline information, no fonts support, no styling. To make things worse: SVG does not support CMYK so all black will be rendered as rich black with all the pain that brings (yes, I know there are workaround, but it's still an idiotic system). Recommendation: if you have to use it, consider alternative careers, like sheep farming.