I've been wondering the same thing, and so far, there doesn't seem to be a clear explanation from Apple on how this works. As far as I can tell, there is no waiting period for swapping iCloud accounts on a device. The 90-day waiting period seems to be for swapping iTunes accounts. And at this point, at least half the people reading this will be wondering "What's the difference between iCloud account and iTunes account?" Yeah, it's a big mess.
Basically, iCloud is for syncing and backing up, and iTunes is for buying stuff. Most people will have the same login for both, but you can log in to different ones on the same device. And as far as I can tell, you can still log in and out of different iTunes accounts within the 90-day waiting period, though I've been afraid to experiment with this, because I don't want to get stuck in the wrong iTunes account if I'm wrong. Anyway, the 90-day waiting period only seems to affect automatic downloads of iTunes purchases. That is, you buy a thing on one device, and it automatically downloads to any other device on which you have auto-download turned on.
I could be wrong about this, but that is what I've been able to piece together from my experiences. But even if I'm right and it only affects auto-downloading, it's still a nuisance when trying to sell or pass on an iDevice. I think you should call AppleCare and ask about this, perhaps if enough people raise the issue, Apple might do something to allow for a procedure to waive the 90 day period when device ownership is being transferred.