I had this exact question myself a little while ago, so I’ll share what I learned. I don’t know your level of knowledge with these things so forgive me if I’m explaining things you already know. And spoiler alert, the answer is “technically, but not how you’d like”

An EPUB “file” is really a folder containing a bunch of individual HTML files which hold the text for the book as well as things like the table of contents, and photos (if your ebook has pictures), with CSS for styling. This is the exact medium you’d work in if you were designing a web page, but with en ebook there are different best practices and considerations.

Now assuming that your PDF has a good OCR (optical character recognition) layer, then it will be possible for calibre and other programs to grab the text of the PDF, and even to create an epub with it. But as you’ve noticed, they don’t do a good job of this. The fundamental problem is that creating an epub is something of an art, with best practices and personal choices as far as layout and file structure. When you “convert”, you’re not changing the file type from PDF to EPUB; you’re grabbing the text from the PDF and then sticking it into multiple different files, with HTML and CSS instructions throughout to tell the EReader how to lay things out, which footnotes link to which annotations, where to display pictures, etc.

As far as I’m aware, this basically can’t be done (well) with dumb, automatic programs like what Calibre offers because there’s too much “thinking” involved. Perhaps an AI tool could be created that would handle this better, but I’m not aware of one, and it’s a pretty specialised application so it’s possible you’ll need to wait a while before someone gets around to that.

So I realised that if I wanted an EPUB version, I’d need to make it myself. I used Sigil, a free EPUB creation tool, to do it, which gave me some nice features to help speed up the process, but it’s a big time commitment (unless you’re working with a very short PDF), especially for your first EPUB where you’re still learning what to do while making it. You’ll also need to learn HTML and CSS if you haven’t already.

I did it as a sort of fun side project in my free time to learn a new skill, but unfortunately other than that, I don’t think there’s such thing as an “EPUBinator” that’s gonna take your PDF and create a well-made ebook.