My view as a heavy ebook reader: ePubs should be inert data. No javascript, no interactivity, no network resources. Just a fancy text file with some appearance settings all of which the reader can override.
Think about what javascript exclusion means, and all the things a good universal ebook format needs to support. Nicely rendered math? Currently the best option to do that is embedded mathjax (maybe you could pre-build mathml and ship that, but I'm not sure that covers all cases). Graphs or charts? There are nice js libraries for that, while doing it manually means exporting images or svgs. Even static svgs are annoying and brittle to font-size changes without javascript to adjust the svg size appropriately.
Don't confuse what's necessary for standard fiction books with what the format should support.
JS and interactivity are fine, in technical books, reports, or niche fiction.
What I absolutely agree on is that epubs don't need is networking. Resources on the internet get stale after years or decades anyway, so inclusion of any network assets into an epub guarantees that the work will degrade over the years. References can be web links, but nothing from the internet should be embedded.
Sure. That doesn't mean an author would want to maintain MathML inside an ebook.
a) What epub editor software allow direct editing of MathML, and is it a good idea to depend on such software being available in order to edit the book without tinkering directly with the MathML by hand?
This describes several existing formats, from Markdown to XSL-FO to the (rather niche) FB2 which is a glorified XML that supports some base64-encoded images.
