Designing a matching network with biasing inductor
How do I set up the circuit to measure the impedance as seen from the
  transmitter that includes the biasing inductor which is connected to
  the supply?


That inductor is shown below inside the red box: -



Is often called a "radio frequency choke" or RFC and its main function is to block RF signals at the PA out whilst providing dc bias to the collector of the PA output transistor.

To that end you can ignore its presence in a circuit like this and, assume it is open circuit for AC signals.

However, if you are intent on taking it into consideration then the 100nF, 220pF and 680 pF form a pretty good low impedance to ground and, in effect, bypass any worries about regarding the battery terminals as being shorted.

If you have designed this properly (like the above) don't worry about the trace inductance unless you have an un-obvious but compelling reason to do so. In which case, don't be shy, let's here it.