Custom export format does not retain section layouts?

It’s not much work to toggle the switches to where they need to be, but is it normal for these options to not be retained in a custom format? Is there a way I can ensure they’re saved and carried over?

Saved, yes. I don’t know what you mean by carried over.

When you compile, the format is saved, or if you change the format and do not need to compile, use ⌥ and the Export button changes to Save. If neither of those options keep your changes, something is very wrong.

Carried over in the sense that I had book one in a series set how I wanted it, I then load the project file for book two, but the section layouts are not set in the customized template.

The Section Type → Section Layout assignment is specific to each project + Compile format combination. In fact that’s sort of the point: you aren’t committed to a specific “look” until you are ready to assemble an output document.

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If you File/Save as Template, I think the layouts should carry over. Or you can export a format in Compile in one project (in the screen where you see formats on the left) and import it in another project. Don’t forget to assign section types to layouts, if it’s not already done.

A new Compile format can be saved as either a “project” format or with “My Formats.” Project formats travel with the project, including any templates created from it. “My Formats” are specific to a given installation of Scrivener.

I knew that, but I didn’t think of it because I always use project templates.