Yeah, except mobile computing kinda changed that dynamic, as did desktop browsers.
As you pointed out, a "backup" is only useful to a point if it also relies on a master cloud. So your backup may have taken place when you had Version 10.4 of Birds with Friends, but if the current version in the cloud/store is 10.6 when you restore the backup, that version gets pulled (with exceptions for your version of the operating system, in some cases).
It's more of a crap shoot than I'd prefer, but such seems to be the way of mobile computing (and auto-updating desktop browsers). At least my desktop computer is backed-up regularly and I never auto-update the operating system.
"Desktop computing" is slowly becoming an anachronism, so the future aught to be interesting...