From setting up templates to help a leader organize group thinking and create an action plan, here are some insights I gained that may be helpful to others who also wonder when to use a matrix versus an idea set:

To set them up, matrix rows can be easily imported from a spreadsheet, and they can also be created from the lists in other tools, like idea sets.  However, a matrix column cannot export to another tool, and other tools like idea sets cannot received pasted or imported data, and in that sense, I think of a a matrix as the last step or destination - "not a through street".

Each idea must be entered into an idea set one-by-one - I find it takes alot of patience sometimes to intialize a starting set, especially if there are several biins and numerous ideas or issues, and then keep it organized, especially if bins change as the group shares.   However, the ideas can themsevles be cascaded on to a variety of other refining tools, including a matrix - so I think of an idea set is a first step down a path with many forks. 

I hope this thinking is correct - and that if it is, this view might be helpful to someone else.