Even with this assumption, which I strongly disagree with, something like unchained where the company holds at least one key so they know the money is actually there, ought to be in order.

What would really be in order though, is a distributed custody internal to the company between the finance department and heads of the company. Now obviously they aren't running their whole company on Bitcoin, but if they were, the way to handle that would be to have the departments use distributed custody between the managers of each department and the finance department, because departments have budgets and those budgets are tracked by finance, therefore, this setup is appropriate for the use case.