I think the confusion is why you’re setting the “page break before” in the contents section rather than using the Separators tool to do that. With the defaults in the Standard Manuscript format, folders designate new chapters and have a page break before them, set in the separators–on ebooks, this will appear as a section break, and each chapter will thus be in the auto-generated TOC. It sounds like you’re trying to additionally make every scene within each chapter appear in the TOC, so you will need to change settings for that, but you could still do that just with the separators and add a section break between text documents as well. (Although here’s where a screenshot of your binder would help, so we could better understand where the section breaks are required.)
True in that case you’d want to have a different set up for the ebook compile and the print compile, ebooks with section breaks between text, for example, and print with a custom marker between text so your new scenes don’t start on new pages, but since you can save the compile settings, you’ll only need to set each one up once and then you can just flip back and forth between the saved settings. In neither case should you need to set a hard and fast page break before in the contents, so flipping between settings will work fine.
This set up would give you the section break between scenes for ebooks instead of the custom separator, so maybe that’s also part of the confusion? Meaning, when you compile for the ebook, if you want both a section break (so the section appears in the TOC) and a custom separator, you’ll have to put the custom marker somewhere else–I’d suggest as a title prefix for the appropriate type and level in the compile formatting pane (click the “Title Settings…” button to add the prefix). Even if you choose not to compile the title of the document, the prefix will still be included, and you can thus add your hash mark or what have you there. Like the separators, it will be saved as part of the compile settings, so you can add it for your ebook compile settings and not have it when you switch to your print settings. I’ve never seen anyone need to do that–most authors publishing to ebook formats just have the chapters show up in the auto-generated TOC (which is sufficient for the reader to understand it), with the chapters starting a new section and without a custom marker between them–so it didn’t immediately occur to me from what you were saying earlier, but if that’s what you need it should be doable.