We can see the work going into these, as one who has modelled warships in the past (and now still modelling and making construction plans for actual vessels)
Shipbucket drawings take a lot less time per drawing, although if I count research times some might actually come closer then you would think
No requirement of course, but it might be interesting to try out ideas with the shipbucket scale, because while drawing takes time, editing and trying things out is a lot easier then in a 3D model.
As for the CIWS. I am typing this from memory, so I am not 100% certain, but it should be about this: the USN considers ESSM as an anti missile weapon, similar to CIWS, or at least they did during the development phase. With the end of the cold war, the risk of missile spam attacks was a lot lower. So, some variants of the burke design even had no Phalanx at all! with the phalanx block 1B the phalanx got an anti-surface mode as well, which made her more of an multi purpose weapon. that is not unlikely to be the reason why there are still at least one on board.
The spaces underneath the phalanx positions are in use for non-CIWS equipment, and need more redesign to be removed then to keep in place. Additionally, if needed, you can just bolt a phalanx on top of them without the structure used on the build-with-phalanx positions.