Kobo readers are really two readers in one. They have their Kobo-specific rendering engine for "kepub" epubs, that's really nice and has all the features you mentioned and is epub3-compatible. Then they also have an ancient version of Adobe's rendering engine that just kinda all around sucks but allows you to load Adobe DRMed files from other stores if you want.
There is a
plugin for calibre that will "kepub-ize" your epubs when you sideload them, allowing you to take advantage of most of the Kobo renderer's functionality (you don't get some stats, but you do still get dynamic page numbers, % read and time to completion estimates for the current chapter and the whole book, better rendering, etc). The caveat is that the plugin won't work with DRMed books, so you'll need to de-DRM your books before sideloading (I'm assuming you're already familiar with removing DRM). Like you, all of my books are sideloaded, having come to Kobo from a Nook and thus most of my library was purchased from Barnes & Noble. The plugin works great for me, and I've never even bothered to try the Adobe renderer.