If you made things properly modular, you'd be able to get a module for the new equivalent component and some convertor that would make it work.
ARM chips are ridiculously backwards-compatible (even if you had to tie to it an onboard RAM module too), you could make GPS modules just talk NMEA over the wire, batteries haven't changed that much that you couldn't at least supply and equivalent or smaller battery module (even if it meant also changing the "charger" module).
The problem is that you've just made... a phone. That was obsolete in 4 years. And costs more than a normal phone. Quite what you've gained, I have no idea. Does the fancy "green" ethic hinder getting equivalent replacement parts by any chance, or ramp up prices? Yeah, that's why people don't do it.
I wouldn't pay THAT much more for a modular phone, because at those prices the whole phone becomes "modular". Throw it away and buy another of the same type, or just buy two to start with.
But I cannot see a reason that you couldn't bundle everything in a fixed-size package, talking a standard I2C, and then just literally clip 2/3/4 GPS modules into the phone and have it talk "your" protocol over a shared bus. The only thing that differs is the battery but - again - if you want it modular and replaceable, made the battery module be "charges from 5v, provides 3.3v" and put regulators in the module so it doesn't matter what battery you use.
It would be slightly chunkier than a new phone. Modules would replaceable AND upgradeable. You'd be able to lock down cheap knock-off modules if you wanted to. You'd be able to move to an entirely new battery tech, GLONASS/Galileo chips, etc. with just a module change and (maybe) a software update.
But if it's just going to be another throwaway phone in 4 years, I'm not sure why you'd bother at all to have any kind of niche phone.