Beyond the fact that I don't see S-E allowing multiple simultaneous log-ins with a single account (see: no discount), the question of being allowed to run multiple simultaneous instances of FFXI on a PC is a red herring. Virtualizing a system capable of playing FFXI is trivial on a modern computer.
It doesn't matter if you have multiple FFXI windows open or multiple VirtualBox/Virtual PC windows open, the result is the same.