An installation of an in-flight wifi hotspot, or mobile phone cell, requires a supplemental type certificate (STC). During the STC process, the potential for interference is evaluated and the aircraft's systems are modified as necessary in order to meet certification requirements. Limitations are established prohibiting the use of such systems during departure and arrival, and procedures are developed for mitigating and dealing with any interference that does occur including the ability for the pilots to disable the system when interference occurs or is suspected.

The in-flight phone systems, which aren't (yet?) in use in the US AFAIK, are designed so that by having the "cell site" so close to the phone, the cell site can keep each phone's output power at it's lowest level--a function that is integral to the mobile phone systems. By contrast, a phone used in an airplane without such a system will ramp up to its highest transmit power setting due to the difficulty in establishing a connection at altitude and from within the metal fuselage.