I’m asking for a specific type of joint for sheet material. Woodworking isn’t the best fit, since my question is not limited to plywood. Engineering or DIY seems like too broad a match, I have no hope of getting answers there.
Specifically my question is — how do I calculate the size of a cutout for such a joint so that a wrench would fit?
What you are describing is a part of engineering design. Ensuring there is sufficient clearance is a common engineering problem so they should be able to help.
Disclaimer: I’m not on Engineering.SE but I am a professional engineer.