However, I am now using Scrivener 3 and there are videos that show how to create a custom TOC by creating a new text file, and copying the file structure into it using Edit / Copy Special / Copy for TOC, and paste.
Okay, it sounds like that video is either incorrect, or perhaps misleading, as that command you are referring to is not what you should be using for ebooks in the first place. You will note that it also copies page number placeholders—which don’t do anything in an ebook, and it makes use of tab stops to offset the page numbers, and tab stops don’t exist in ebook formatting either. So it’s all rather unsuitable to the medium.
The advice given in the user manual section I referred you to is the only correct way to make a ToC in an ebook. Basically the capability being granted for a custom ToC in ebooks is not to create a fancy design in the editor, but rather supply a different list of sections than the automatic generator would. That’s all it’s for.
I looked for a box to check that says leave as it is, but all I have found is a box that says N/A. There are options for heading, section, and a few others and then a box for N/A. I could not find any thing for leave as it is, as was in the previous version of Scrivener.
This is all a red herring. To rephrase what was said before in a more technical and direct way, there isn’t a way of formatting the ToC like you’re thinking of, because it’s not normal content. It’s a special piece of data that in part helps drive ebook reader software navigation, like when you use a button that advances to the next chapter.
That is why CSS is the only way to create custom, fancy ToC designs.
But that aside, to answer your question about as-is, there is an “As-Is” default layout that is always available in the Assign Section Layouts screen. For normal content that would pass-thru editor formatting through.1
1) Since it sounds like you’re looking for older conventions in the new software directly, at some point it might be helpful to check out the migration tutorial we’ve written, which among many other small changes, shows what happened to “as-is”, “page break before” and so on.