This is only an issue with C and C++ written applications that aren't recompiled or rely on x86 specific opcodes, the .NET ones will just run, unless they rely on native code, of course.
Hence why they are doing a JIT this time around, but as we all know Intel isn't happy about it.
The x86 emulation is completely irrelevant. Microsoft didn't want win32 applications to be recompiled to run on Windows RT. They now changed their mind. The only benefit of emulating x86 is for software that is no longer supported. If it's mission critical then those businesses that rely on x86 backwards compatibility will stay with x86 hardware because paying $600 more for a computer doesn't even register on their radar. The only reason I'd care about x86 emulation is to run old video games.
It is completely relevant. Basically, you can now replace aging Windows PCs with VDI hosted on ARM clouds, and people won't know or be able to tell a difference. You will now have x86 Win32 apps, arm64 Win32 apps, and UWP running on what's just another SKU of Win10. And since every piece of software for Windows must support 32-bit x86, there is full backwards comaptibilty. You won't need to wait for some mission-critical bit of software to be ported, and in the Windows world, there is plenty of mission-critical abandonware, trust me. Now it gets the AOT/JIT treatment. Microsoft just made enterprise a reality for ARM64 servers by crossing the proverbial rubicon. Suddenly, if you use Windows and Microsoft products, you can still buy into ARM data centers and clouds.
It doesn't have to be about the cost of a computer but e.g. getting field workers onto Windows tablets with decent battery life (but still being able to use the ancient in-house timeclock app)
Hence why they are doing a JIT this time around, but as we all know Intel isn't happy about it.