External BSP models have their own lightmap, which is not lit by world lights.
Put ammo boxes in a dark area of the map, and they'll look terribly out of place, because they will still be lit as if they were in a bright area. That's worse than MDL lighting.
Makaqu 1.6 fixes that by using the lightpoint value of the world to change the lightmaps of the external BSP models; I don't know of any other engines that does this. However, that solution isn't as accurate as making those models part of the world's BSP.
For some of the other engines, as Spike said, you can use full real time lighting, which is slower and doesn't look the same.
Teleporters and telepads usually don't move, so there's no point in separating them from the world. And in an ideal scenario, there would probably be no external BSP models; exploboxes, ammo, health, etc would all be prefabs compiled within the map. Too bad the default progs.dat doesn't support that.
By the way, the .origin of inline BSP models being '0 0 0' is atrocious, because it ruins things when we want to make an inline rotating BSP model that's properly lit, since afaik BSP models only rotates around their .origin.
Ph'nglui mglw'nafh mankrip Hell's end wgah'nagl fhtagn.