Hartington,
The short answer is that restrictions to electronic devices don't apply to approved equipment. When an electronic flight bag is installed in the airplane, it's been thoroughly tested for function and interference. A dedicated approval is given to the individual operator, for each specific airplane.
We use EFB's, though not Ipads. Approval took about two years and was not a simple affair. The FAA looked at utility, reliability, safety, interference, redundancy, effectiveness, and so on, and did a very thorough evaluation of the individual units, and their application and use in the airplane. Each unit was tracked by serial number and tested and tried. The approval is for use in the cockpit. We don't carry them around the airplane with us.
Personal electronics have potential interference issues with avionics and navigation equipment. Hundreds of cases have been recorded and reported of electronic interference. Shutting down and securing your unapproved and untested equipment when asked is important for your safety and mine.
We have a lot of electronic equipment in the cockpit, from instrument displays to navigation radios. We have radar, communication equipment, electrically heated windows, and various power sources, converters, inverters, rectifiers, and so forth. Everything in the cockpit has been installed, tested, and designed to function together. We know what to expect. Even the magnetic compass is tested and calibrated with the equipment operating so we know the effect that all the installed equipment will have.
When I sit down in the cockpit, I have to turn off my personal electronic equipment, too. The cell phone goes off. I use an electronic noise cancelling headset, but it's approved equipment in compliance with a technical standard order (TSO). When you're asked to turn off your cell phone and power down your equipment in the passenger section of the airplane, it's for good cause and you're in good company; pilots do the same thing, except for approved, necessary, and compatible equipment.
You're asked to keep your equipment off until we get above 10,000', when you're often told you can turn your equipment on. During that time, climbing to 10,000 or descending below that altitude, we have our own restrictions in the cockpit. We don't even engage in non-essential conversation; instead we maintain a "sterile cockpit." Safety rules are for everyone. They're applied a little differrently. You can talk in business class or coach, for example, whereas we are focused on the business of getting you somewhere safely. We don't talk. We can use an approved electronic device which is instaled in the airplane and tested and authorized for that installation, whereas you don't have that capability or permission during critical phases of flight. We all do our part. Consider keeping the electronics off to be doing yours, and we do appreciate your helping out.