Apple moved from 68k to PPC, and then to Intel. Binary transitions like those are not new, and are made easier by an OS that is architecture agnostic from very early on.
It's not so hard for the OS to be architecture agnostic. Linux runs on lots of architectures, and also Windows NT was portable enough to run on MIPS early on and also runs on ARM in addition to x86.
The main challenge is seamlessly migrating users to the new platform and Apple did a great job at it using Rosetta.
Both Linux and especially Windows struggle at this because they lack something as well integrated as Rosetta and require all applications to be recompiled to a new architecture.
Microsoft could have ported Office to MIPS, Alpha, PPC, and Itanium. I don’t think IE ever had a PPC port. The same applies to Visual Studio. When Alphas started appearing, that’s all I needed to be happy - a way to use email, to browse the web and use Altavista, and Visual Studio so I could write programs. It’d be a different story.
