Here is a how-to on best practices for manipulating text flow on the screen. I have no idea what a “horizontal rule above a page break character” means in terms of Markdown conversion to ePub. That doesn’t sound like a clean solution to me, more like the proverbial broken watch showing the right time.
As to the rest, I don’t really know. I can’t explain why 1,2,3,4 comes outs as 3,1,2,4 when you compile. As always I recommend looking at what Scrivener actually creates, by compiling to .md and opening that in a text editor. That sounds to me like the topic of another thread though—probably a bug report if you can demonstrate how to compile the incorrect order without settings design to do that on purpose (Collections as compile group).