Why would you convert an epub to pdf? There is no ebook reader, other than kindles (for which the proper conversion would be to kf8), that can't handle epubs.
On the contrary! Why would you ever keep an epub file around? If somehow an epub file finds its way into my computer, the first thing that I need to do is to convert it to pdf to be able to read it with a reasonable viewer (or print it!). After the convesion, I delete the epub file; I really dislike this format and the associated software.
Why prefer an epub...
They have flowed text, and ebook readers let you customize font and font size so that the book's text adapts to you rather than you adapting to a particular combination of publisher quirks and zoom necessary to fit in a particular device's or app's viewable size.
They're generally smaller files.
And if there's something about the epub you don't like, you can actually fix it.
If a book is available in both PDF and epub formats, it's a reader's prerogative to pick the one they want, and there are specific types of books where PDFs might be preferable. However, if there's no original pdf, what is the objective of converting an epub to pdf in order to read it on a computer? Whatever you think you're accomplishing, I think you're mistaken. You end up with a pdf that looks exactly like how a typical ereader would display the epub. Minus the flowed text and font customizability, and probably with poorer navigation as well.
Does epub support proper proper math notation typesetting?
Moreover, text in a webview doesn't flow as nice as vanilla TeX, and can look outright atrocious.
Also, modern unicode fonts have good coverage of math symbols, so a lot of abstract math can be written inline without even resorting to mathjax. Algebra, set theory, and things like that.
I think the delay there is the many older ebook readers and apps that have quirks that require workarounds to get mathjax to work. Why bother, when publishers could just render equations to images or SVG and hardcode them? Mathjax just takes that rendering step out of the publishing pipeline.
Text flow... are you talking about inter-word spacing and rivers? My take on that is: full text justification was always a bad idea, only promoted for aesthetic reasons and to show off fancy layout engines that reduced rivers and other bad artifacts. It seems some publishers are doing away with it in new books. Poetry and plays rarely used it.
I would say that mathematicians are extremely picky about the quality of their displayed formulas. Most of what can be produced by mathjax is not of acceptable quality. I speak about fine-tuning of kerning, alignement, etc. Having "reflowable" text is a nightmare for typography-inclined people: the flow is an essential part of the content and you do not want to lose it!
Back to the main points:
Epub is a better format for everything except niche uses (textbooks, especially math, papers, etc) where there's an argument for pdf. It's rather weak, but I understand the argument and I don't throw a fit when such material is only available in pdf. Most regular books aren't even published in pdf format anymore, for good reason.
There's no reason to convert epub to pdf except to print it — and why the hell would you do that? buy a used print copy — or to send to someone who doesn't have an epub reader — in which case you're better off giving them the name of an epub app to search for and install, so that they can read epubs in the future, rather than converting every epub you want them to read into poor quality pdfs.
Meanwhile, mathjax will only improve, along with publishers' general css competence.
a) EPUB supports Math notations
b) you don't even have EPUB files where it's an issue.
I've tried to like them, customize them, fix their problems, etc but to no avail.
I prefer epubs too, but apparently readers really like PDFs...
Which is also its downside when formatting is not critical. I want to be able to change the font size and have the text reflow correctly. With PDFs you end up with broken layouts if you don't view it exactly as formatted.
Reflowable books also do a poor job reflowing content.
Case in point, the free AWS ebooks on kindle are a god-awful mess whenever they add code snippets, no matter how small.
Given the choice, a good fixed format layout beats a bad reflowable layout.
There are all kinds of potential use cases for users of differing levels of technical sophistication.
Why wouldn't you provide an option to convert to .pdf?