And not to be too petulant, but "I don't think it has all the information we might need" isn't the same as "has none of the information we might need". Maybe there aren't good accessor functions, but it clearly has some information that you clearly do need.
As near as I can tell "Total Freeze" is Flight Gear lingo for "pause". It seems to pause the simulator, and there is no "pause" option that can be mapped using the dialog. It seems to correspond to what the 'p' button does. It's possible there's a distinction, but I don't know what it might be.
I can certainly understand that it would be unreasonable for the dialog to "edit" a hand crafted configuration file, but "can't base it off the previous default one" makes no sense whatsoever. You mean to say that you cannot query the simulator to see what it's currently using? It's clear that the simulator is using the correct assignment because it has pulled it out of the default file. But the dialog can't figure that out from the current simulator in vivo? That makes this sound like a design issue....
"Joystick Configuration" breaks joystick settings