Ok, I am not anywhere close to being an expert in Rhino,I'm a novice at best. With that said, I could be wrong but I think Boolean is not a tool to make bulkhead with.
With a simple shape like a fuselage or a ship hull:
1: Surface > Offset Surface > Distance(input your paper thickness, my default is 0.01") > Flip All( if arrows pointed outward) >Hide the outer original skin.
2: (Cut the copy to make a bulkhead)Surface > Plan > Cutting Plan. (With the copied skin selected, cut the cutting plan and delete the copy if you don't need it anymore and what you got is a bulkhead.
For complicated shape I would not use Offset and make a copy, I will Cutting Plan the original to get the bulkhead I need. After I cut the shape, Select the shape:
1: Curve > Curve From Object > Duplicate Border(then delete the shape)
2: (With the new line): Curve > Offset > Offset Cure(Input your paper thickness)
3: (With the new cure I don't use Surface > Patch because Patch doesn't like to patch complicated shape. It will come out all wired. Cut the new

cure instead)
Surface > Plan > Cutting Plan. ( delete the outside are of the cure and you got a bulkhead.