Yes, the District charges Disney fees. (Here you go:
http://rcid.org/DoingBusiness/PermitsFees.aspx) There are 'walls' between the two. Even though the District is supported by Disney, it operates independently and acts like any other municipality would. I believe the planters were done prior to the building simply because the vendor was already doing the same stone planters in the completed areas going down the strip towards the Boathouse. They just did the planters as part of the plaza after they did the faux turntable and pavers. The top planter isn't part of the building, it's on the plaza, but will be incorporated into the patio of the restaurant. The bottom one is adjacent to the wall of the building.