I suspect the fees aren't always about cost, but rather a subtle encouragement to customers to do certain activities.

I had a bike bag weighing 27kg and a second piece weighing 15kg. Well under the 46kg I could take on for no charge.

The airline (Qantas) wanted to charge me an overweight charge for the bike bag - but were happy for me to park in front of the counter for 5 minutes while I moved heavy items between bags to balance them out.

I didn't really care; it was a financial motivation to keep my weights at an easier to manage level.

I imagine that overweight bags require different workers, who might be on a different pay scale - and so there is a cost to moving 27+15kg vs 22kg+20kg.

If you have double the items of luggage, you need double the number of handlers to move it through in the same amount of time. Excess baggage isn't all about the weight, it's a just a convenient and public-understandable thing to focus on, and gives them incentive to pack less.

Baggage storage is very limited and usually packed full way more than passenger cabin space.