However once the phone has reached the user I do not see at all how open protocols reduce Apple's appeal to people who want to exclusively use Apple software. You can simply do just that.
Would Microsoft be more valuable if we all could only install software through the windows store and the OS was locked down? Nobody would claim that. Third party apps are what adds marginal value to the phone. This is precisely why Apple let's third party developers put apps on their phone, something that Jobs for example initially opposed. He wanted to build everything in-house.
I think Apple is valuable for a lot of reasons. They have a great sense of aesthetic, user friendliness, UX, great hardware, but I do not believe at all that a lack of software raises the value of the phone. If you had a universal chat app that interfaces with all other proprietary protocols on your phone right now, your phone would be worth more.