Is it possible\allowed to have the flue exit the house close to
the ground but then have a 90 degree elbow to take the flue
and air intake up the wall to an acceptable height - perhaps
even to the eaves?

No problem. In fact, it is often only possible with a condensing boiler, as
the flue operates at such a low temperature.

You may have trouble getting rid of the condensate in a cellar installation.
Consider a condensate pump, such as a Sanicondens, to pump it away to the
drain. Do not accept the condensate just dripping onto the ground, like most
cowboy installers would have you believe is acceptable.

Christian.