I just tried out my first epub book (Breaking Dawn by Stephenie Meyer) and noticed that it uses an embedded font.. at least, I'm pretty sure it's embedded. It's not my custom flashed font, nor does it seem to be Times New Roman (although maybe it is..?) It also has the actual page numbers in tiny script on the very right side in appropriate places. It's also left-aligned, not justified. Page turns are fast though, despite the embedded font. Very interesting.
P.S. I do, however, miss being able to customize margins and text size and font as I would normally through Calibre. I miss justification and having a little bit of white space around all the borders (my own preference, I just like it that way.. not a lot, a slim margin). Up til now I bought .lit books and converted to .lrf.