Can you make the text of folders not appear when you do draft as scrivenings?

I use Scrivener in conjunction with Aeon Timeline, which will rearrange Scrivener’s file structure when you rearrange it in Aeon Timeline. That function works fine, but when it puts scenes into folders, the folders are also treated as documents. I get that this is a feature, not a bug, but is there any way to make those blank “documents” not show up when I select draft>display subdocuments as scrivenings?

I use Scrivener v1, but this is actually enough of an annoyance to me that if it can be fixed in v3 and not v1 I’m willing to upgrade.

Unfortunately, a Scrivening displays all selected documents. Regardless of whether they are marked as to be included in compile or not.
There is (to my knowledge) currently no way around it; even in V3.

This being said, in your case we’re only talking about a title and an empty line.
How bad is it?

You could use a collection (leaving the undesired out of it), but you’d have to constantly rebuild/update it. Not worth the time invested, if you ask me.

Now that I think of it (in V3 - V1 was too long ago, I don’t remember if that would work),
you could insert a designated symbol in the title of the documents you want in your scrivenings (only those) and use search results (searching for that symbol) to spawn your scrivening, by selecting all files (as easy as Ctrl+a) in the search result list.

You can later have that symbol be automatically removed from compile.

In v1: go into Tools ▸ Options..., and in Navigation disable the Include enclosing group in combined scrivenings setting.

In v3: go into File ▸ Options..., under Behaviors: Folders & Files, try disabling the Include enclosing folder text in scrivenings mode setting.

That should work. But only if none of the desired files have other file(s) nested in them.