Occasionally I've been known to make epubs out of PDFs. It's painstaking work and it takes hours to comb through each page manually when doing this. (There's a few on LibGen of my work like Blood In My Eye by George Jackson and Dimitrov's Selected Speeches, from the publishing date prior to this work being heavily edited in the post-Stalin era.)
The thought of someone undoing all that work almost makes me want to cry lol.
I use ABBYY uhh... idk the rest of the name of the app and I haven't installed it since I transitioned over to Linux so I can't find it rn.
I'm not even sure what the difference is between ToCs. I figure it's just a nice thing to have links out to the chapters within the epub at the start. If you feel like explaining the difference I'd be the most willing audience.
There are inline tocs, and toc files (EPUBs are just ZIP files with a different name and a file which defines where all the other files are in the zip). ToC files are used by readers when the user asks for the ToC (e.g. right clicking in calibre and clicking on Table of Contents). Whereas inline is like in printed book, where it will show up on one of the pages.
I haven't used ABBYY so I don't know how to do it in that. But Calibre (which I do use) has an easy "Insert inline ToC", which will take the toc file and insert it as a list