LEED CI Project Boundary - Non-conjoining Spaces

We have a project for a single entity that owns and occupies an entire building. They are required to achieve LEED silver on this renovation per their local code. They wish to renovate two distinct areas that are non-conjoining and on different floors of the building. Area 1 is a full interior renovation to a distinct office area and seems pretty straight forward. Area 2 (which is much smaller than Area 1) renovates three rooms that are non-conjoining on the lower level of the building. One of the three rooms in Area 2 is a large auditorium and the work in that room is isolated to one portion of the room, new lighting and finishes for their stage. The owner plans to use a different contractors on Area 1 versus Area 2. The owner's hope was to rate Area 1 & Area 2 together under the same LEED submittal. Some questions we have: 1. Will Area 1 and Area 2 need to be rated separately? It seems like the answer is yes since they are under separate contracts. But since the owner's preference is for one rating, I thought I would double check. 2. Regarding Area 2, will it be a problem for the auditorium to be included in the certifying floor area, since only one part of the room is being renovated? If not, can the work in that room be excluded? I don't want to fall into a trap of create an onerous review process.