Brett - you are correct in that NT-class systems support DOS programs
only through virtual machines. In fact, all programs other than certain
parts of the OS itself run through virtual machines; that's fundamental
to the architecture, which attempts to prevent all possible interference
of any app with any other app or with the OS itself.
There is a breed of DOS and other programs that cannot run in a virtual
environment, usually because as coded (sometimes by design and sometimes
by bad coding) such programs absolutely require direct hardware control
to execute successfully. This will always be prevented and such programs
aborted by the OS.
Applications originally coded for a DOS-like or native environment (say,
a realtime control app of some sort in an important environment like a
factory or a hospital) will either have been recoded for a high
reliability multitasking system, or will carry caveats warning against
running them in any but native machine mode (self-booting, for example.)
I believe there may be some multiboot managers - probably obscure - that
will allow switching betwen OS's via on-the-fly keystrokes, and perhaps
you could find and make use of one. It would be a Very Good Idea to keep
in mind, if you do so, that this may open the door on such a machine to
corruption and mayhem via introduction of unexpected mods to code and
hardware conditions that might cause unreliability and loss of integrity
in the more sophisticated OS or in that app.