I don't use the Reader, so am not up to date on everything that can be done from there. I think it's criminal that it does anything more than show a blog excerpt/teaser and a link to our blogs where they can read the full post, Like it, Share it, and/or comment on it. You make an excellent point that it totally devalues all our efforts to create a nice-looking blog. And it really discourages paying for a premium theme, although I broke down last month and did it anyway.
Good points about the site complexity too. There are fine points I forget about or don't fully understand (that keep getting changed without any notice to us!). And I got tangled up with the Customizer recently, trying to do something with my header, when in fact everything I needed was already on my dashboard. The Customizer doesn't work properly in many cases, and conflicts with dashboard options in some cases. It's no wonder newbies can't figure things out.
Worse, although you and others make valiant efforts to answer questions in the forums, apparently many go unanswered (I've posted at least 4 in the last two weeks about image sizes and display, with no response at all.)
Bottom line ... yes. It's all understandably very confusing and frustrating for new bloggers.