Why the layers
You generally don't need all of your bones in the MD5. Much of the armature in a moderately complex setup is helper bones, which need to be filtered out. What you suggest results in all of that fluff ending up in the export result. This is not what I would want, but if you're OK with that, just put them all in layer 5. That's one keypress and one click.
Are you aware that active bones layer can be exported? Leave it up to artist to have a layer active with bones he wants to export. It can be any layer, as long as it's active. If you load MD5's from Doom 3, you will see that there are bones in them that ideally should not have been exported.
The idea that artist has to put bones into layer 5 is ridiculous, because everyone has their own habits and workflow. I might want my export bones to be in layer 1 and someone else likes to have them in layer #last.
The messing bit
There's a script included in the readme to help stuff the MD5 layer.
That's besides the point. Making awkward workflow and saying "go read docs" is not a user-friendly approach.
Tough. But then, how are those constraints more severe than in other exporters?
There are no other exporters besides one for 2.49, where you can pick out what you need to export, where you need to export, etc. etc. It's more productive, it's more intuitive, more artist friendly.