No one thinks that their boss has the power to rearrange physical reality at a whim.

It is a very common feature of bad bosses that they think they have the authority to order their underlings to rearrange physical reality. This seems to be exactly what's going on in the original post.

it reads like this: "Because my job performance may be affected by the laws of physical reality, which my boss is powerless to alter, he (the boss) in fact has no power over me!"

The fact that the speaker is addressing his boss directly changes the meaning a lot. I'd read it as "No matter what official authority you have, if you order me to violate the laws of physics then the laws of physics are going to win." Referring to the mice as his "real boss" is an attempt to explain why he's constrained by the nature of reality to someone who spends a lot more time thinking about org charts than about the nature of reality.