This really takes us off-topic, but there are “done is better than perfect” solutions. Here is one I’ve used in the past. It’s called PDF Index Generator. The results need some tweaking, but it’s not bad: https://www.pdfindexgenerator.com/ It creates more of a concordance than an index; the problem with a concordance is eliminating common words that don’t relate to concepts.
Other than as a user, I have no relationship with the company that makes the software. I’m well aware that indexing is a profession in its own right, there is a society of professional indexers in the US. Indexes for law books are atrocious–they must want lawyer-indexers and I bet there are few of those. When I finish the book I’m working on, maybe I’ll set the program on the Scrivener manual and try to tweak the results.
But the truth is, the OP had already checked the right box in the Options tab. Their screenshot shows that to be true, because otherwise the does Facing Pages item would not appear on the list in that dialog box at all.
What confused was the rather natural expectation that the new item called “Facing Pages” referred to both recto and verso pages and hence that controlling the headers/footers of both would be there in that place.
I think the point is well-taken. ‘Main Pages’ and ‘Facing Pages’ seem like non-optimal names for the case. I assume a judgement was made that ‘recto’ and ‘verso’ were terms too recondite to use, but maybe ‘right’ and ‘left’ could have done service there. Or even have Facing Pages handle both, just like the OP expected. Either solution would smooth things out a bit.
True, and I’ve complained repeatedly over the years that there’s no reason to call them “main” and “facing”. Both pages face the other, and there’s nothing more important about a “main” page.
My point (if I had one) is that users need to look at what’s in front of them, hover over icons for useful hints, search the manual for the words they don’t understand, and try things. It seems intuitive, to me, to click on Facing Pages to see what it’s about. You’d (not you, but anyone) immediately see an alternative location for headers and footers; if you typed in it and compiled or looked at the preview, you’d have an answer. Or you could search for it in the Manual.