Hello there. You're absolutely correct that the EE edition is time limited and is not an OS that qualifies for upgrade. They were explicit in explaining that before downloading. However, they did allow one to use it again for another 90 day cycle. I don't remember how that was performed. I'm not sure if they allow that any longer.
The only edition that the MS online store offers is the upgrade whether Windows 8 or Windows 8 Pro. One must have a qualifying OS to upgrade to whether it be through Upgrade Assistant or fresh install. One cannot use the qualifying OS any longer otherwise it is in violation of the EULA.
I ended up buying the 64 bit Windows 8 Professional OEM System Builder edition on another online store for $105 U.S. MS online store does not offer the System Builder editions. I'm going to dual boot with 7 and this is legal under the EULA of that edition. This was confirmed by MS in online chatting with a rep and his supervisor. It's also confirmed on package when I received it. A stand alone installation situation is legal also.
Hope that helps.