I think that the point about fragmentation in the smartphone (Android) area isn't an exact allegory for the "x86/64 / Windows" history. Here's what I think the concerns are about the issues that Android Phone faces compared to iPhone:
1. Screens sizes / resolutions etc. This isn't the same as the "x86/64" issue with a windowed environment because of course the res of the desktop doesn't matter if you're running something in a window, or even if you consider full screen running applications on the "x86/64" as back then of course we were using CRTs which would all (to an overwhelming degree) be 4:3 and run at 640x480 or 800x600, at 60Hz, and so you could write your full screen app to use one of those common ones. It's not the same on a smart phone, especially with various screen ratios, and LCDs which do have a native resolution to look their best.
2. Processing power. This is the same as the "x86/64" issue, and of course that was a nightmare at the time - having to check every single piece of software before you invested to make sure that you met every one of its requirements or it'd not install, or crash, or be dog-slow.
I'm not saying that there aren't reasons the other way, where Android Phone beats iPhone, just that these are the two main reasons that people think of, I think, when they say "fragmentation" of Android in a way that doesn't affect iPhone.
I'm also not saying that there aren't ways round these, there may be, but I'm not a programmer.