Your iPhone is not "registered for the developer account"; instead, you have membership in the Developer Program, which allows you to create Provisioning profiles.
The Provisioning Profile contains a list of device identifiers (UDIDs) and allows applications created to run only on these devices.
One device can be specified in any number of Provisioning Profiles. However, Apple limits the number of devices for which a member of the program can create profiles, so you do not start to bypass the App Store.
In other words, your iPhone is not tied to your developer account. Rather, the apps you create are tied to your iPhone. Your iPhone can run applications from all developer accounts, as it has a place to install them.
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