I only sideload to my Kobo. I never use the desktop program, have not bought a book from them and now have my wi-fi turned off. As you can see, I'm their most valuable customer
Advanced font control can be enabled for side-loaded fonts with a patch. As mentioned though, advanced mainly has to do with the weighting of fonts. Font size, line spacing and margins are available whether you patch or not.
I think Beyond the Book only works on books purchased from Kobo. I've never used it. I use Calbre to manage my metadata and collections.