I generally agree with everything you mention here - but where do separate level lumps come into play here?
They don't in this particular example. The seperate level lumps we just carried over from the WAD design into the ZIP design.
We didn't set out thinking "I know what would be useful, seperating the map data lumps" that just kind of happened, we didn't sit down and spend time designing stuff to do it (other than the lump ordering which seemed like a good idea anyway so...) - it was a natural by product of the new (much more organised) design that we were implementing anyway. It's no problem, most users won't even see a benefit to that in the case of map data lumps but the feature is there if anyone has a use for it.
In Doomsday the ZIP support is completely intergrated with the WAD support and Lump Assemblies into ONE virtual file system where ALL files/lumps are treated equally. This means that lumps in WADs sit alongside files on your HD and those loaded from ZIP inside one big virtual directory.
Within this virtual filesystem DD_DIREC (WAD directories) and
-vdmapings (both physical and virtual) can alter the virtual directory organisation from the outside and by users (this allows us to (among other things) completely change the physical Doomsday installation directory and still support mods written for much older versions of Doomsday which relied on a particular directory structure. It also allows users to remap any folder on their HD inside Doomsday's virtual file system).
Also, just like everyone else, I think that in general, releasing new maps with all of the maps' lumps dumped into a zip instead of a wad is pointless. Creating your own map editor and encouraging people to do this is also a pretty pointless exercise.
You have to consider the bigger picture. Doomsday mods contain stuff like models, hires textures, particle generator definitions etc etc (none of which HAVE to be put into a WAD (but they can be). Interestingly none of our users EVER use WAD when they can use ZIP...). so authors naturally use ZIP anyway. So using a Lump Assembly they can work directly on their mod in a folder somewhere on their HD without having to constantly import data in/out of a WAD/ZIP file.
So look at it from their perspective. All the while they are working on Doomsday specific stuff in a Lump Assembly - living is good, they can use whatever programs they are comfortable with to do their editing Photoshop, 3DStudio, Notepad, Explorer etc however as soon as they need to do anything within a WAD they then need to use small niche programs like XWE (which may not even be available for their platform) constantly. This really slows down the work flow and I fully agree with them.
In the case of map data it really isn't even an issue since you never manually work with the map data lumps but rather than saving the map into a WAD an editor could just as easily save the map into ZIP, which would then go into the Lump Assembly as a unique, single entity.
I really don't see what the issue is against 12 files in a ZIP as opposed to 12 lumps in a WAD.
So you'd use it as a means to circumvent the permissions that are given to you. Yeah, right. I'd say the author has the right to place such restrictions on his map as a whole and that'd make such mods as questionable.
Thats a different issue really and perhaps beyond the scope of this disscussion but yes, one of the things we are aiming for is the ability to patch any map using additional lumps not part of the original I/PWAD. For example, we could fix that shotgun zombie bug on DOOM2 MAP02 using a THINGS patch lump (it would only contain the changes). No patching of the IWAD required and the distributed patch lump would not breach any copyrights.