Have a look at this post, which describes the various conditions required to get rid of section breaks entirely, and revert to plain page breaks. As I note there though, depending upon your workflow, the best answer might be to switch all manual brute force page flow settings off in Separators. Depends on the software you’re moving on to though.
The previous version worked this way as well, by the way, but it had fewer triggers for it, and so you might just never have encountered it, or had deliberately simplified the output back then and haven’t yet done so with v3.
As with the previous version, whether you get section breaks or page breaks is an all or nothing thing. Scrivener is incapable of determining when they should be used, and when they should not, so it just spams them everywhere a page break would go. It means its settings (such as swapping out header content per chapter) work as advertised, but as you note, it produces a quite rigid and difficult to work with document when attempting to introduce it into a flexible design workflow.