I can’t figure out how to style block quotes. I see the “Styles” pane, but the sample text there doesn’t match what I’m seeing as output. The format is also different for each section type.
If we’re talking about styled text in the editor, then I don’t know how you’re ending up with different formatting depending on the section layout. It is the Styles pane that governs what styled text will look like when it is compiled as a global setting (advanced stuff aside, like custom CSS which can completely ignore every setting you make with the GUI, should you wish to). But to briefly clear that point up: absolutely, Scrivener is not WYSIWYG—styles in the editor are for you, not your readers or the printer or anything else that has little to do with you writing a book. Of course if you please, you can make it look like it will in the end by leaving any declarations out of the Styles format pane. But the whole idea here is that you can very easily compile two completely different looking documents from the same source material.
Alternatively, if you have a custom metadata field called “Epigraph”, and you’re inserting the text of that into a template output via a Section Layout’s Title Suffix field, such as “<$custom:Epigraph>”, then absolutely the Layout can change the formatting. Custom metadata doesn’t save formatting, so the injection is plain-text, which will take on whatever formatting you have set up for the Suffix in the Layout.
That aside I would create a simple test project that shows how to get these results, and attach it here. There are too many different permutations involved for me to speculate on how these screenshots were created, let alone how to normalise them.