A followup e-mail I received on this topic:
One clarifying question I have now is: given that only one transition can happen per cell per time step, what determines the order of operations? Which of the transitions has a chance to happen first, second…. and possibly exclude other transitions from taking place?
Within each primary transition group the non-spatial model iterates over all cells and and for each of these considers simultaneously which, if any, of the possible transitions for that primary group will occur. The algorithm is such that there is no bias towards one transition group excluding another. In the most recent version of ST-Sim, users have the ability to specify the order in which they would like the model to iterate across primary transition groups. The order can be specified as iteration and time varying. If the order is unspecified, the model randomizes the order each timestep.