Well I deal with a lot of boxed upgrades as I deal with a lot of SMBs and what happens is it gives you the classic "this software is not genuine" when you get to the desktop on first install.
After that you get the fun of either dealing with a MSFT flunkie over the phone or just using the bootloader hack, frankly I'm leaning toward the latter as I'm tired of dealing with those motherfuckers on systems where the key is either plastered to the tower or in my hand in the retail upgrade box. I've already got several customers looking at Macs and Linux because they do not like how untrustworthy MSFT has become and I've started running various distros in VMs looking at exit strategies. MSFT? Be fucked.