Apple ID 90 days waiting on MacOS, too

I thought this was supposed to work differently on MacOS than any of the iOS series. Basically, if a person has two separate ID(s) from original iTunes and .Mac era, then iTunes, Xcode, and iBooks are supposed to treat them separate and equal even if they coexist on the same Mac and same account.

Also, how is this supposed to work for "family" Macs, classroom Macs, etc? Sure, the iOS devices make sense as they are very personal to each person. But, a MacBook much less a desktop Mac might have a family of users on them, each with their own Apple ID.

For users going back a way to cheetah and jaguar, this is an issue as they used a different ID for .Mac from their iTunes. I was told then that these IDs were supposed to be able to coexist, even as we for a hunger iPhones and iPads. The only way I can see this happening is for a cross over issue between iBooks/Xcode and iTunes. What do we humble users do now? Can we now finally merge accounts? This seems to be a big issue as far as I can see.