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Does MS consider Apple's Boot Camp to be a virtual machine?

I don't think so. As I understand Boot Camp, it is basically a nice GUI to set up dual-booting.

You're right that Boot Camp is not a virtual machine; one is running Windows on the bare metal hardware.

Boot Camp does provide three technically useful pieces beyond the GUI setup:

It puts all the Windows drivers you will need for your Apple hardware on a CD, for ease of use with Windows, and to save you having to scour the internet for drivers.
It makes it easy to repartition your disk, to make room for the Windows partition.
Most importantly (many geeks can deal with the above two on their own) is that Boot Camp upgrades the firmware on your MAC to provide BIOS emulation. Native Intel based Mac's use Intel's Extensible Firmware Interface (EFI), which is totally incompatible with the BIOS's that almost all versions of Windows (excepting the Itanium IA64 version) are built for. For a look at EFI from the Apple perspective, see How Apple’s Firmware Leapfrogs BIOS PCs.

You can also get the firmware update separately from Boot Camp -- see Apple releases firmware updates for all three Intel Macs.

Beware that this BIOS emulation is not perfect. For example I see this post discussing problems with getting the disks to operate using the highest possible performance with this BIOS emulation, because it is doesn't enable some of the advanced disk channel options: Mac Pro w Boot Camp - SATA, AHCI, EFI, BIOS - what can we do?

I'm not active in the group of folks doing Linux ports to Mac Intel hardware, but (1) I'm sure they are active (Linus Torvalds, the King Penguin, drives a Mac Intel for his main box), and (2) I'd imagine that they are working with "real" EFI firmware, not the Boot Camp BIOS emulator firmware. Linux has long supported EFI booting; that I know because I've been doing it for several years, on Itanium hardware. EFI is frequently the provocation for some of Linus's finest rants on the kernel mailing list lkml.org.