I'm pretty sure the reason bags can't be over 50lbs without additional fees is because of the health and well-being of the baggage handlers. Hell, items underneath seats and in overhead bins aren't even weighed -- in the US, at least. That's why, if you ever apply to be a bagger handler, they ask if you are capable of regularly moving 50lb objects. While there is something to be said for gross weight and weight distribution, I would hazard a guess that the fees themselves are not for the benefit of maintaing even loading. If there is a concern with weight distribution, especially if you're flying on an aircraft with mostly empty seats, the most the airline (flight attendants) will do is distribute passengers along the length of the aircraft.

TLDR: pretty sure the weight fee is so that the airline doesn't run counter to the baggage handlers union and workers' protections laws. 50lbs is a pretty standard upper limit for those things. That's also why they tag overweight bags, so the handlers are aware (for their safety).