The problem for B&N is that some of their reader apps (the BlackBerry for one) don't currently support ePub. So if they send out one file format it has to be eReader.
Last time I tried, downloading an ebook within the Windows B&N app will still get the ePub version - even though a web browser delivers an eReader version. This isn't possible on the Mac (where the download is always done by the web browser).
I do fault B&N for not reporting if a given ebook is available in ePub format. Amazon does the same with AZW vs TOPAZ, but Amazon should say too.