You've misread the problem.
Apple DOES have an X86 ecosystem AND an ARM ecosystem. They do not cross streams and customers are not confused, and Apple can successfully grow application ecosystems across two very different architectures.
So what is Microsoft doing wrong?
It's very simple, and I cannot believe they haven't already done this. I'm thinking that the naming scheme for their ARM platform is why they're balking, since they've stupidly named their ARM ecosystem "Windows Phone".
Apple succeeds by maintaining separation between the ecosystems, and that's where MS is failing.
MS needs to realign:
Surface means x86 tablet. Period. End of story. It's a high end tablet for those who need more than an iDevice, who want a full laptop in a tablet shell. Surface means quality. Surface means x86, and it means desktop compatible.
Windows Phone, including Windows Phone Tablet (Surface RT) means ARM. Period. The WP8 ecosystem and it's tablet arm should be the branding covering the ARM ecosystem.
I'm thinking that the name "Windows Phone" for the ecosystem is what dissuaded them from trying to attach the tablet to that ecosystem.