Tone and Spoike, what I said before about -keeplights wasn't entirely true. It seems it's a switch that works exclusively in -onlyentities mode, although I feel it should work in the -meta phase, it doesn't seem to want to budge.
But anyway, if for whatever reason you still want to include rt lights directly in your map, just run a second -onlyentities compile (this is a phase switch that works on it's own, so add it as it's own entry in your build scripts/menu) and append -keeplights (no caps) and it will compile the entities INCLUDING lights.
EDIT: seems to work with nocaps in -meta, which is strange since it didn't do that for me before.