These two are likely because normal members cannot place water/lava on their own. Because of that, if these were unbanned, some random passerby would be able to remove the water/lava a manager placed in a build at the builders request. Similarly, world grief is against the rules, and having access to sponges would allow people to remove the natural water/lava generated around the map.
Because map builder perms aren’t given to trusted members, it’s given to members that have made a map. You don’t need to be trustworthy to do so, and it’s definitely not an act that is going to make you any more trustworthy on its own. Couple this with the very lacking moderation of Build as a whole and it’s not worth the effort it’d demand to make sure the perms are in the right hands.
Yes, I believe Quinci placed a global ban on these a long time ago due to the duping glitch, and the fact that they hardly ever seemed to be used outside of survival.
These two I don’t think anyone knows the reasoning behind, besides maybe Rofle.