A very good point. I also use the same method as you do, but you probably know how flaky this can be sometimes, too (At least if you use all this: Gmail, G+, Analytics, Google Music).
You are right that there are cases where you would absolutely would want to have completely separate accounts. That's why I would like to have this as an option: Linking two "services" from different users, or attaching two users/emails to the same service.
As it is right now, Google+ for Apps is mostly useless for anyone who already has a G+ account. And I don't think that Google really wants to release mostly useless products.
You are right that there are cases where you would absolutely would want to have completely separate accounts. That's why I would like to have this as an option: Linking two "services" from different users, or attaching two users/emails to the same service.
As it is right now, Google+ for Apps is mostly useless for anyone who already has a G+ account. And I don't think that Google really wants to release mostly useless products.