@Narrsd: thanks for taking the time to investigate this. Yes I do generate the TOC manually (by selecting all the sections I want to have in the TOC in the binder and copying them into a Table of Contents section). Unfortunately I can't make any manual changes after that, because we're publishing non fiction with dozens of chapters, sections and subsection (first volume is 470 pages long, second volume is 250 pages long) so it just has to be handled.
Then if I have to do anything with Scrivener Mac to compile, then I'd rather use Scrivenenr Mac for everything, We output from the same manuscript directly to EPUB for kindle and to PDF for print to Amazon KDP and Ingramspark, which is why Scrivener is so amazing in the first place. So there is no way to collate different outputs into one file, and frankly we don't have the time to deal with this kind of workaround when releasing a book, which often requires frequent updates in a hurry. Anything that slows down or can cause errors is not an option during a book launch. So Scrivener Mac is used now.
However, we'd like to leave the Mac platform and go back to PC. There is no way this can be done given Scrivener PC current state, and the fact that compile is still completely unusable.
Unfortunately even the font issues you mention have not been resolved.
I have reported this issue with the Special Elite font months ago: viewtopic.php?f=57&t=57740
It's still there. Apparently it's not there if you create the section in Scrivener PC, only when the manuscript was created on a Mac, which means that it might never be resolved as it seems to be good enough for the team to ask Mac users to recreate sections that the PC version can't handle properly.
Basically compile is still not functional as far as I can see. It's been the case for months, and although a few of the reported issues have been fixed, we're still a long way from being able to use this. Every time I try to compile my test document, it still looks like a broken experiment: no title page, wrong spacing for some fonts, errors in TOC... Just garbage.
I have no idea what the priorities are for the devs, I'm just hoping that issues like these are not forgotten, and that by the time it moves out of beta all these issues will be solved. In the meantime, we have to keep the Mac to release our books. We released the last one in October (on the Mac), let's see if the next one (in the first half of 2020) can be released on PC.
I'll check back in a couple of months, when it's time to decide on which platform we do the formatting