Your post is fine, it’s just that it has been the weekend.
Markdown just creates HTML files. That is its sole purpose, and thus anything that can be done with HTML via CSS is available. CSS isn’t something you control from Markdown, it’s purely a stylesheet applied to the content. All Markdown does is describe said content. So strictly speaking: no, it doesn’t let you indent paragraphs because the full extent of what it has the capability of doing is saying: “this is a paragraph”. The expectation is that one would use styles to take the raw semantic blocks and make them look pretty, though. So practically speaking: yes you can indent paragraphs. 
The same goes for MultiMarkdown, the extended syntax of Markdown that Scrivener makes use of internally. Both of these formats follow an idea of deliberately not allowing one to declare things like indenting in the writing medium itself. All of the styling using these tools is done with stylesheets. For example, in CSS you could do something like this:
p { text-indent: 3em; }
h1 + p, h2 + p, h3 + p, h4 + p, h5 + p, h6 + p { text-indent: 0; }
That will indent all paragraphs by 3 units of measurement relative to the font size (so the size of the indent will scale with the text proportionally), but on any paragraph that immediately follows a heading of any level of depth, no indent will be used.
The attached .txt file you provided shows two paragraphs declared as quotations. Typically, browsers will display quotations as having a block left indent of around half an inch, but this varies. Naturally one would want to use CSS to handle them more nicely. Whatever the case they are not intended to be a way of saying a paragraph should have its first line indented, if that is what you are going for. Your paragraphs should be standard paragraphs. Again it is the CSS that declares what a paragraph looks like, from the font all the way down to the metrics of the margins, indentation and other factors. For example, the way the blockquote element appears in this forum post, with a little quotation mark symbol, straw coloured background and faint border.
You definitely wouldn’t want to use a tab in front of your paragraphs, if that is what you mean, because that tells (Multi)Markdown to make the line a code or verbatim block.
Regarding Markdown and e-books, the creator of MultiMarkdown has designed a script for converting an ordinary MMD document and turn it into an ePub. The script can be found at this location.
One would work using Markdown (and optionally MultiMarkdown) syntax while writing in Scrivener, and when they compile, they would choose the plain “MultiMarkdown” export option from the “Compile For” drop-down menu. After that, Sigil makes a good editor for working on the CSS (as mentioned above, for defining the look of your e-book) and other polishing aspects. Finally, you would open the finished ePub document in Kindle Previewer to automatically convert it to a Mobi file, suitable for Kindle distribution.
So, if you want to stick with the Markdown route, that’s a good way to go. Otherwise converting your Markdown files to HTML/RTF and importing them into Scrivener for a traditional rich text workflow will be fine, too. It’s mostly a matter of taste.
