Can I use Linux as both a native system and as a Virtual Machine interchangeably?

Possible: yes

Easy: probably not.

I have booted windows disk images via qemu, so nothing is impossible. Linux will be more tolerant of booting in different environments (virtualised vs native) and as long as the libs are there for each, it shouldn't cause too much trouble.

Your best bet would be to hypervisor both windows and *nix.

Alternatively if you want to "try before you buy" - write a copy of your nix partition to an ISO (dd) or duplicate it to a vdi with your software of choice, and try booting that.

More directed help could be found if you specify what emulation software you are using (Virtualbox, ie), and whether your CPU supports nested paging or virtualisation.