To add to the idea of experiment there is an interesting option, yet I have still to test, is the possibility of using Autodesks Beast to make ones own lightmaps if you are using 3ds Max
to mak UrT HD maps.
An expensive solution for the stand alone version but Unity 3 does come with Beast (free version included) and since fstech1 is not a closed edit environment with assets being native to Urban Terror one could export to FBX, import into Unity 3, create custom light maps using Unity to remap UVW's, export from Unity as OBJ back into 3ds Max and then out to Gtk.
I'll be looking into it myself but figured it's interesting enough information that others might want to experiment with the possibility as well.
I was thinking about something similar a while ago but never got around to properly test it. This Beast looks like it basically just uses a second uv set with a texture that has a rendered lightmap baked in. I'm just thinking, can't 3ds max do that too? I know blender can. The question just is, has anyone successfully imported a model with multiple uv sets in radiant/urt yet? I haven't.
If that's what beast does, you can't use obj to get it into max because obj can't save multiple uv sets correctly.
You could bake all your lightmaps in 3ds Max but it is a veryyyyyyy time consuming process where if you mess something up you more or less have to start over again.
Small maps should not be to much of a issue to do in Max, GrandHall was done using render to texture, but Beast handles all of the uvmapping and packing for you based on the targeted number of images you want as well repacking the UVW's.
As you said though OBJ could be a problem but I'm assuming the repacked maps are on UV channel 1 or you can move them over to 1 just like in 3ds Max.