Many problems: First in regards to VMs, if you have to emulate actual CPU you need to run the client OS you can just throw any/all hopes of decent performance out the window.
Second, software doesn't just magically re-write itself properly. In order to work on specific hardware as well as it possibly can it has to be properly optimized. Some of the clearest examples I can point to are in the gaming world. The PS3 was notably hard to program for, hence most developers didn't bother using the hardware properly, while a few did. The really good PS3 titles look damn near as good as many titles do today on the PS4 and compared well with the best PC titles of the era; they even supported things like stereoscopic rendering. The worst titles looked like absolute crap and you would swear you suddenly has a PS2 again. Within the PC world this is why game "a" will look and run beautifully on moderately powerful hardware but game "b" will run like crap on better hardware and might not even look as good. So software needs to be properly optimized to run as well as it possibly can, and this takes time, and money, and talent.
Now, what happens when you are a developer writing software for the 85% or 90% Intel/AMD based market? Do you actually go out and spend the money you have to spend to properly support that company that switched to their own CPUs? Welllllllll?? Probably not. You probably get the software working and that's it, because there isn't enough reason, financially, to do otherwise. A few companies will do in anyway, but most won't. So sure, that great "Apple CPU" might be 10% or 25% or hell, even 100% faster than an Intel/AMD CPU, but that doesn't mean the software will actually run faster. We are actually likely to see the exact opposite in many cases, unfortunately.
I would say this , I cant believe MS will want to get caught napping through another transition , you might think that Apple moving to ARM is not a transition , but if MS sits on their ass AGAIN like they did with the phones , and then some small company that only have a search engine comes along and uses another obscure san diego company that makes ARM chips to create a better then avg chromebook , something that will be competitive with the MS offering , gives it for free , open source , light and capable , full suite of office apps , what might happen then? SoftBank are pushing for performance , cloud infrastructure is being developed , mobile is a lost war now for wintel.
MS are using android for their mobile HW for god sakes , they will not let that happen again , i cannot believe they are THAT arrogant to just ignore the world around them , they will come on board and in doing so bring everything with them.
If you are a SW developer house that thinks like MS of the past , that nothing can touch you , then you will soon see the competition coming for your lunch.
I believe you are looking at the tip of your nose instead to the future , ARM is here to stay not sure how everyone just keep ignoring it , it has major traction from 2 of the 3 leading OS`s in the world , it has 3 out of the 4 biggest tech companies developing HW and SW for it (Amazon are on board).
MS will not be betting all the marbles on Intel/AMD (X86) , as they did in the past and got obliterated out of the most profitable market of our Era.
Again , look at the big picture my friend , its not apple alone that will make the SW houses (primarily windows) support ARM , its the other players in this game that you conveniently left out that will drive them forward by hook or by cook