I've had a few more thoughts on this. I'm tending towards it being
Spoiler Catherine's house rather than James's - either something she inherited, or something built for her. Something that she and James started to use as a lab but then realised wasn't safe enough and then abandoned to move to Rivet City.
I've come up with some ideas for rooms:
The main body of the house is divided into four "towers" leading off from the main reception hall. I have decided to allocate the rooms in each tower as follows:
North Wing
* Four bedrooms, each with an antechamber
* Four bathrooms
South Wing
* Drawing room
* Library
* Music room
* Upper hall
West Wing
* Chapel
* Dining room
* Kitchen
* Reception room
East Wing
* Dormitory
* Entry to bunker
ScrapCave
The bunker itself would house
* Workbench
* Hospital
* Laboratory
* Armory
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