We are in the process of updating the online documentation for ST-Sim. The new home for ST-Sim documentation is docs.stsim.net. We have already ported over a copy of the old documentation here. For example the current documentation you are looking for is at http://docs.stsim.net/reference/prop_transitions.html
That being said the documentation for Transition Simulation Groups and Transition Multiplier Types is pretty limited at the moment.
Transition Simulation Groups: during a spatial simulation ST-Sim iterates over each transition simulation group to generate “events” for that transition simulation group. Events can be a mosaic of transition types within the transition simulation group that is being generated, therefore you should only combine types within a transition simulation group that you would expect to be part of the same event. Transition Simulation Groups could be useful for combining other types of transitions. For example, you could have different level of severity for insect and disease transitions which could form a mosaic within the same outbreak “event”.
Transition Multiplier Types: these are used to break your Transition Multipliers into different types of multipliers. ST-Sim then combines (i.e. multiplies together) all the multipliers from different types at runtime. For example you might have a multiplier type called “Historic Annual Fire Variability” that represents a multiplier accounting for the annual variability in Fire probabilities observed historically for your landscape. You might then have a second multiplier type called “Fire Future Trend” that represents a trend in the overall increase in your Fire probabilities over time. At runtime ST-Sim will combine these two multipliers to give you a net multiplier for your Fire Transition due to both annual variability and future trend.