Refurb products are usually excluded from a lot of promotions. Such as student discounts, the back to school 100$ Mac App store stuff, the free iPod promotions they used to do, etc.
When I bought my refurbished G4 iMac back in 2003 it shipped with OS X 10.2 Jaguar and I qualified for a free (I had to pay for shipping) upgrade to OS X 10.3 Panther through Apple's Up-to-Date Program. So there's a pretty good chance that Lion will be available to those who purchase a refurbished Mac after June 6th. Keep an eye on this page OS X Lion Up-to-Date Program for details on how the free upgrade will work and to see if refurbs will qualify.