How is the potential difference between the outer and inner surface of the glass bubble in a glass electrode measured if an Ag/AgCl wire is used as the indicator electrode and Ag/AgCl/KCl is used as the reference electrode? In the Nernst equation for the reaction, hydronium ions don't participate.
You measure an electric potential difference. It can be considered sum of three different effects. If you could isolate them, you will have the electromotive force of both reference electrodes. If they can be isolated, each of them will generate a potential difference at open circuit (when the stationary state is reached) equal in magnitude to the emf. You always will have this difference of potential plus the potential difference at both sides of the membrane. Just add potential differences due to the stationary condition reached because of the emf.