AGPS just means they download the almanac via a mobile connection, however they do work fine outside of mobile coverage, just need up to a few minutes until they get their first fix. However, in iOS devices the GPS is part of the mobile chipset and therefore can only work if flight mode is off, something that is not recommended on board of most airlines.
And yes, the field of view form a flight deck is pretty small while the window heat shields most of the weak GPS signals. Dedicated GPS units work most of the time with reduced precision and mobile phone/iOS units sometimes work but not really great.