I get your workflow, but I'd make a couple of suggestions:
1) That's a fine strategy. We're talking book construction here, not InDesign document construction. But that leads to:
2) Depending on the size of the chapters, you may want to consider making each chapter its own document. This gives you more flexibility dealing with folios, page/chapter numbering etc. It's just as easy for InDesign's Book functions to assemble 20 chapters as it is to put together, say 4 sections. But if we're talking lots of tiny chapters (I just laid out a set of book guts with five sections and 50 chapters between 2-4 pages, with a running page count of 180-odd pages) that may be more trouble than it's worth.
3) It's not necessarily required to break down an InDesign document for each chapter, but it does make life much easier.
Another way to do it is to break folios off the master page layout for "exceptions", like Command/Control+Shift+Double-Click with the mouse to convert the master page folio into a page element, and then copyedit the exception into the layout. This is what I did with the micro-chapter book I described previously. But then it puts things on you to maintain document consistency rather than InDesign's automatic book functions.
Another option is to build unique master page layouts for each chapter to let InDesign maintain document consistency across the section, but you still have to apply the appropriate page masters to their respective pages. Lots of people like this workflow, but I find it easier to just release the master page folio item(s), make my exceptions, and maintain the document consistencies myself. Your mileage may vary.
4) You can build your InDesign documents out of multiple sections, but I'd advise against it. For a number of reasons, I prefer to break a book layout into as many small, discrete and consistent chunks as I can, then use InDesign's Book functions to snap things together for your book guts. You can learn more about how InDesign's Book functions work here:
https://helpx.adobe.com/indesign/using/creating-book-files.html
Hope this helps,
Randy