Maybe the dev's can code separate .ent files to store exclusion areas, killbox and other minor "pach" stuff to fix problems on maps. This way you dont need to edit BSP files, rebuild BSP, edit internal entitys, etc... you distribute new .ent files with the fix entitys.
This separate .ent file will serve, also, to spawn more eggs or other stuff as needed, to balance minor problems, and to change slighty the gameplay. Nowdays we have only a few maps, and small changes can be good, i guest.