I like the new Compile window!
However, it seems an abstraction too far to distinguish between Section Types and Section Layouts. It’s really confusing to be able to define Section Layouts, but then not assign them directly to parts of the document.
But that’s exactly what you’re doing with Section Types and Section Layouts, isn’t it?
You tell Scrivener what you want each element in the Binder to do (be a ‘Scene’, be ‘front matter’ etc) by allocating it a Section Type. Once you’ve done that, you never need think about it again in the Editor, no matter how many different compilation formats you’ll have eventually. With your scenario, you’d be constantly going back to the Editor to reallocate the layouts.
Instead, in Compile you simply say 'format all the scenes (Section Type = Scene) like this (Section Layout), format all the front matter (Section Type = Front Matter) with that Layout. When you compile the document, you are given the list of all the Section Types you have defined and all you do is link them to the appropriate Layout. If you don’t like the default layouts (and they cover a lot of the most common scenarios), then you can edit / create your own.
The beauty is that once you’ve defined the Section Types for a Project, you can compile it to any output format you want, simply by allocating a relevant Section Layout to it (either one of the default ones, or creating your own) in compile.
E.g. In Version 2, if you wanted Appendixes which differed from Chapters only in that they had the Word Appendix and a letter in the title, rather than Chapter and a number, you had to try to force that into the Binder structure somehow (Chapters = folders, Appendices = document groups and so on). It was possible, but fiddly, and not really intuitive for new users.
In Version 3, you just allocate the Section Type Appendix to one, and Chapter to another, then choose / modify the appropriate layout in Compile. It’s conceptually much simpler, but it also makes possible a lot of more advanced differentiation if you need it.
But it is a different way of looking at compilation, which is why it causes experienced V2 users a bit of disruption until we get used to it.
Thanks for the kind words! We’re still in process getting the new compile set up in Windows, but I’m excited for all it’s going to offer. As Brookter said, it’s a big improvement over how compile worked in 2.x on the Mac, and it’s going to be an even bigger leap from 1.x on Windows, so it may take a little time to adjust to the new way of looking at this, but once you grasp the concept, you should see how this offers a lot more flexibility–and ultimately less work–than the previous method.
By separating Section Types and Section Layouts, Scrivener is letting you define what the parts of your project are–something that remains constant: your scene is always a scene, your table of contents is always a table of contents–and then use any number of different compile formats to choose how to format each of those types. You can quickly produce a PDF, ebook, or Word document from the same project all with unique formatting appropriate to the compile type, and switch among them without having to reset the formatting each time.
Likewise, you can use the same compile format for multiple projects without having to force those projects to use exactly the same binder construction. It becomes less fiddly–instead of having to reshuffle things to make sure your folder and file levels match up with the compile formatting or vice versa, you just slap a layout on each section type and you’re done. And you’re able to think about the parts of your projects with meaningful names (“scene”, “chapter heading”, etc.–you can customise it however is meaningful for the project), so it’s a matter of saying “I want to format scenes like this” rather than “I want to format level 2+ documents like this”. 
Keith wrote an in-depth blog post about the redesign (from the macOS perspective) which you can read here. As we go on with the beta, you’ll be able to experiment more with it directly and hopefully start seeing the benefits!
Thanks for the explanations. It is certainly really powerful and once I got my head around it, I could see the utility. However it is still very top down, favouring a particular kind of learning style.
One small change might make it easier to assimilate on the fly: add “(define new)” options to the all the Section Type dropdowns and lists.
That may not be there yet in the Windows version, but on the Mac, anywhere in the Editor (Binder / Inspector / outliner etc) where you can allocate a Section type, there’s an Edit… item which allows you to create new ones.
In the compile, every item in the binder can be allocated one of the existing section types (but you can’t create a new one – that wouldn’t be appropriate because formats can be shared across projects…).