The plans you found on BeeSource are the right dimensions for a bee hive. From those dimensions you can make a hive. The “Box Joint” file refers to a process for making the “finger joints” that many people use to attach the wood sides to the wood ends. I agree with you, I don’t see that file over on BeeSource either.
If your boss is a wood worker, he/she should have all the info really needed from the BeeSource plans. You don’t have to make finger joints to hold the boxes together, I just use simple butt joints and screws. Some people like to get fancy and make more complex joints: lap joints, finger joints, dovetails, etc. Yeah, those are better joints, but simple also works fine. This is where your boss has some creative leeway: he/she can use whatever type of joint he/she wants.
I would just print off the plans and tell your boss you would like 5 hives ASAP :-D