Unlike Java Edition, BDS relies on all the files in the ZIP or it fails to boot.

It makes sense for the behavior packs and the etc, but the critical files are server.properties, permisisons.json, and whitelist.json. The latter of the 2 can (and should) be generated fairly easily if they are missing (as they are simply empty arrays). As for the server.properties, I'm not sure.

Including these in the ZIP make it harder for updating, as often the ZIP overwrites these files, resetting them. I've seen people have issues thinking their world is gone, but all they did was rename the world and update their server. We also can't not include them in the ZIP, the program crashes otherwise.