As far as I could find, there doesn't seem to be any configuration parameter you can set to make any of the geometric tolerance options default. It's a clunky beast that I just live with.
From the behavior I've witnessed using it, it seems that once you create a tolerance, the numeric value (0.002, 0.010, etc.) is retained from the last one you did. Sometimes it seems like the type of tolerance is also kept, but I'm not so sure about that one.
I suppose if I wanted to not have to click and enter all the settings I want for a bunch of tolerances, I could create one or a set of mapkeys to "preload" the geometric tolerance definition(s) I want to create.