have no fear, richard the old is here. i've got your back.
i don't know where you originated this nor that what you say is the behavior in this forum as I tend to hang out here almost exclusively so far.
what you say though about this structure and the difficulty in figuring it out I can attest to. I probably spent a similar amount of time as you did trying to figure it out, but that was perhaps nearly maybe 4 years ago circa 2012 i think.
i don't know indesign, am happy enough with iba, but it is on my list to learn. i need to juggle between creating more books or more versions of the same book. at my advance age, i lean towards more books. but i digress and this is not likely what you want to hear. let's get to your issue.
i keep the first 4 pages intact. i have a cover of course, an intro media movie and a structure page for my toc. i don't use the glossary. i don't mingle any other pages in there above the line and am even not certain whether one can. easy enough to test.
i then follow this with a copyright page, followed by the dedication page, followed by a preface page as i would say that this is generally what you see in a book. you can add whatever of these pages you want. they will have the same hierarchy as a chapter page but be given roman numerals. i use the copyright page for the copyright, the dedication page for the dedication, but decided that i liked the structure of forward page better than the preface page, so that is what i use for the preface page. note: it's been awhile since i have done this so some details are a bit hazy. i change when necessary the layout by deleting items like pictures when i don't want them in one of these pages. the type of page if i remember is in a text box near the upper left, or that is where i moved it. i must have renamed the forward text box to say preface.
this will generally be followed by your chapter page, section page and content pages, repeated depending on your content. the chapter pages and section page will define your toc.
at the end i have something i put after the last chapter, section and content. it is one of the types of pages you find in the section category. i happen to use the preface page there. it has a roman numeral. i follow it with blank pages, so the blank pages are indented, which is what i want.
hazy, but it appears that any section page will be at the same hierarchical level as a chapter page or else they are moveable in an indent sort of fashion. i don't quite remember and would have to experiment.
i probably gave you enough info so that you can achieve what you want. if you get stuck, shoot me a specific question on anything that my haziness failed to answer or that you are unable to achieve and i will spend the time actually recreating this and send you step by step instructions. but i suspect you will be ok.
io wish i had your knowledge of indesign. i would like to see if it would allow me to port a book to the dreaded other platforms, dare i say. hope it never comes to that but still wonder if i should use it as a backup to iba on the ibook store.
hope this helps.