1. I think some of these are inherent limitations with markdown (e.g. the text/photo alignment).
2. I definitely agree about the keyboard shortcuts in the Rich text editor, it's really annoying how basic things like horizontal rule and block quote don't have shortcuts.
There is an "Auto Format Markdown" option which gives you (limited) ability to use markdown formatting in the rich text editor... but presently it's way too limited (e.g. it won't auto-format basic things like block quotes or horizontal rules), I had posted about this here: Impossible to create horizontal rule or block quote via keyboard shortcuts in rich text editor?
There is a change that should add horizontal rule support coming: Desktop: Rich Text Editor: Auto-format "---", "***" and "___" as dividers by personalizedrefrigerator · Pull Request #12397 · laurent22/joplin · GitHub
3. The hidden toolbar icons issue I had reported as a bug here: which icons are shown vs. hidden in overflow menu changes when toggling editors · Issue #12198 · laurent22/joplin · GitHub
It's pretty annoying, and exacerbated by the fact that there are extremely limited keyboard shortcuts in the rich text editor... things like horizontal rule and block quote get shoved into the overflow menu (despite there being plenty of room), and the fact that I also can't use keyboard shortcuts for these makes it even more annoying.