The main reason is to have more control of how the math equations are rendered (the way softcover converts math to images is best-in-class). I also had a bunch of custom macros and environments that I knew how to do by adapting/extending softcover, and comparatively little experience with pandoc filters.

That being said, I've recently used pandoc for another project (a paper) and I really liked the result and the functionality (references using BibTex). Also, I see modern pandoc has support for MathML and even image math https://pandoc.org/epub.html#math so will be doing some testing to see how it works...