While Nintendo did own 49% of Rare at the time they did not have any control of how Rare built its offices or how the company was run. They obviously had a close working relationship with the Stamper brothers and Joel Hochberg but I don't know of any Nintendo input on general operations.

I'm not sure how you would characterize flashy bullshit, but the Rare offices were basically based on the same premise as the old offices up the road at Manor Farm... isolated developments teams in their own buildings (or at least their own floor) with a central building containing HR etc. Yes there was a full restaurant, but Manor Farm had that too, and it's kinda essential if your offices are in the countryside. The entire office was designed to be a distraction free as possible.

True the building had a bunch of expensive environmental features to help it blend in to the existing rural landscape and to reduce carbon footprint but I'm sure it was way cheaper than building or leasing any kind of generic office space in London or heaven forbid in SF.