My guess is the group of people they have designing missions and scenarios are manhandling the game world for their use-case without any care for the overall consistency. Just think about how many developers "fix" bugs by addressing the symptoms instead of the foundational issues in the code.

Probably goes something like this: we can make these easy-to-use mission designer tools and hire a bunch of interns to crank out content.

Then such a huge mess gets created it takes over a year for the more senior developers and designers to untangle it. Your VIP mission absurdness is buried under a list of 10k other issues.

Hitman level design is probably at the other end of this spectrum.