Yes. And, as you may have noticed, the Loadout.ini even allows you (to a certain extent) to mount weapons you couldn't add manually at all.
Come to think of it, you do not even need splitting up the weapon groups to have an asymetric loadout. Of course there remains the problem that certain weapons are not available all the time...
Modified loadout in 2009:
From left to right: IRIS-T, 2 GBU-12E on a BRU-57, 2 AIM-120C, another AIM-120C, ASQ-173, AIM-7P, 3 AGM-65 on a LAU-88, 2 GBU-38 on a BRU-57 and an AIM-9X
The same loadout in 1984:
From left to right: AIM-9M, 2 GBU-10 on a BRU-57, nothing, AIM-7M, ASQ-173, AIM-7M, nothing, 2 GBU-38 on a BRU-57, AIM-9X
Strange, I have no idea why the AIM-9X or the GBU-38s show up there...
Also, how do I get the BRU-57 smart rack to show up without any Loadout.ini modifcation?