You are correct. Think of iBeacons as kinda of like GPS. They feed you data, not the other way around. You can certainly have more advanced capabilities w/ BLE -- similar to what you suggested -- but you'd have the single master problem.
To comment on your understanding:
The app doesn't need them hardcoded, it can query a server and say: here are the beacons I see, where am I?
Alternatively you can include location information in the data broadcast by the beacon. So one of them can say I'm at the end of isle 1, the other says I'm at the start of isle 1, and yet another says I'm at the end of isle 2. You can figure out your approximate position by their relative signal strengths. They can even have broadcast the exact GPS coordinates of where they are located (hardcoded in them of course) which if I recall correctly Apple can use to update their location service to give you very accurate positioning.
Bear in mind though that beacon data, unless encrypted, is public but even if encrypted it can be duplicated so someone can mess with you by creating a duplicate tag and placing it nearby.
To comment on your understanding: The app doesn't need them hardcoded, it can query a server and say: here are the beacons I see, where am I?
Alternatively you can include location information in the data broadcast by the beacon. So one of them can say I'm at the end of isle 1, the other says I'm at the start of isle 1, and yet another says I'm at the end of isle 2. You can figure out your approximate position by their relative signal strengths. They can even have broadcast the exact GPS coordinates of where they are located (hardcoded in them of course) which if I recall correctly Apple can use to update their location service to give you very accurate positioning.
Bear in mind though that beacon data, unless encrypted, is public but even if encrypted it can be duplicated so someone can mess with you by creating a duplicate tag and placing it nearby.