Okay, I'm computing them that way as well; it seems more scalable since the number of transformations for a given candidate pair within GJK seems fairly constant (assuming the algorithm terminates within a known/maximum number of iterations), whereas the total number of vertices between two shapes can be arbitrarily large.
Going further off topic, you mentioned earlier that you use Quadtrees in your engine. How do you like it? I'm still debating what I will use for my broad phase. I've mostly used spatial grids and some custom spin off of sort and sweep in the past. However this time around I'm trying to go for something more flexible / able to handle arbitrary sized regions. It seems some sort of tree implementation may be the way to go, though updating the tree regularly seems like it would be a pain. I'd be interested to hear your opinions.
P.S. I find it funny how this thread has been like a public PM between us two
Haha. It's nice discussing this with someone who has already faced many of these issues. :)