There's already a patch (due for 4.10) to detect and warn about this silliness. Since the Intel guy says that all the systems that shipped with this mode now have firmware updates to allow disabling it, there's very little reason for anyone to implement full support.
Hopefully in the future Intel will think twice before implementing ugly firmware-level hacks to aid in working around limitations of Microsoft's driver stack.
That's the firmware setting that disables the hack that hides NVMe devices behind the chipset's AHCI controller. Aside from making it possible for standards-compliant NVMe drivers to function as expected, not lying to the OS about the hardware topology also allows the OS to access the PCI configuration space (allowing for eg. ASPM support) and not unnecessarily share interrupts between two entirely separate devices.
If it served a useful purpose in the first place, yes. And if it were properly documented and didn't cripple certain areas of functionality (and probably hurt performance a bit, but I don't yet have a system to measure this with).
Hopefully in the future Intel will think twice before implementing ugly firmware-level hacks to aid in working around limitations of Microsoft's driver stack.