To give a little information on this from what I know.
Having different keymaps is impossible without the use of third party tools as mentioned prior. There is one way it would work but it would require a dev patch and an update to the launcher if I'm not mistaken. Freelancer by default loads all saves and pref files from C:\Users\X\Documents\My Games\Freelancer. It is possible to hijack common.dll to load them from the install dir meaning you could have a "cap" install and a "snub" install each one with a different control set.
By using the following code the devs could change it to allow such.
Offset 0A2FB1: Change 56 6A 00 6A 00 68 05 80 to C7 06 2E 2E 00 00 EB 0E
Offset 0A300A: Change 21 to 0C
Offset 0A3018: Change 13 to 7C
Offset 0A30BE: Change 56 6A 00 6A 00 68 05 80 to C7 06 2E 2E 00 00 EB 0E
Offset 142690: Change "My Game" to "Saves" 00
If devs did that it would load the files from the install directory. This would also move screenshots there as well. Two folders would appear, "Saves" and "Shots". Shots would contain screenshots when you PrintScreen and saves would contain everything else like multiplayer save data or single player saves (including restart.fl which would remove the cross mod crash).
As said before, this means nothing unless the devs add this, which I highly doubt they'd do.
