I would say that the main difference between Scrivener and Ulysses is that the former works more closely with existing Markdown conversion tools (MultiMarkdown which is embedded, and Pandoc which you can optionally install and have integrated) while the latter has its own conversion built-in. I would say that in a way, Scrivener is a “pure” Markdown tool in that it doesn’t have its own markup system that is incompatible with everything else, and if you do want to use these established systems for conversion, it is better for doing so because of that. While you can export Markdown from Ulysses, I’ve heard it’s not the best for that.
So with that in mind, with Scrivener there is ultimately more flexibility because you are working with mature and very in-depth document production capabilities provided by these tools, rather than something we put together ourselves that only allows for a few formats.
Here’s the thing though, you absolutely can just use it very simply. Try it like this: create a new blank project, and paste some Markdown you’ve written into the starter file. Go into Compile, select the MMD → HTML output at the top, and click the compile button. You don’t even have to tweak settings, because at this level of basic usage, all of the formatting is in your Markdown text. And that’s it—and that’s probably why you won’t find many tutorials or discussion threads about using Scrivener that way, because it’s that easy. Want a word processing document? Choose MMD → ODT instead, or install Pandoc and use Pandoc → DOCX (and once you do that, you’ll see ePub as well).
The reason why you see complexity, and technical threads on the forum, is because of what you can do, beyond that. You certainly do not have to, and you can only learn what you want to learn to get something done—you don’t have to ever go all-in. Here’s simple example of what I mean: instead of pasting your Markdown into the one starter file, this time, use the File ▸ Import ▸ Import and Split command, and make sure it is set to split your document by Markdown headers (of course, use a longer document for this test that has headers).
All right, now you’re getting into what Scrivener excels at, and that is composing a long document as an outline instead of into longer files with their own heading structure (more like how you have to work in Ulysses, and most other Markdown-based tools for that matter). With this mode of usage, you aren’t typing ## Heading into the editor, Scrivener is going to be doing that for you based on the structure of your outline. You can move sections around, increase or decrease their indent levels, and all of those headings will adjust automatically for you. When you compile, you’ll need to do a little more setup this time around. Click on the “Basic MultiMarkdown” format on the left, and then Assign Section Types below the preview area. A simple approach is just assign all types to the “Text Section with Heading” layout. This will do what I just described, each level of indent in the outliner becomes a ## Heading with the hash depth worked out for you, followed by whatever text content is in that outline item of the binder.
If you used the same document for both tests, the result should be identical in output. The only difference is in how you work with that text in the writing interface.
So that’s where I would start, and maybe if that’s all you need, that’s where the learning process could end as well. As with most things in Scrivener, you only need to learn something if you want to get more out of the software. Markdown and rich text users alike both have extremely basic ways of using the software that require minimal learning. Thing is, most people eventually do want more, so that is what you see in the documentation and elsewhere. Scrivener scales up to very complex workflows, but that gives you the ability to do crazy things. It would take an awful lot of work to make a simpler tool produce something like our user manual PDF (which is yes, Markdown), and in some tools you just couldn’t do it at all without bringing other tools into the mix.