I was trying to stay away from expressing my opinion on MU but I'll stick my head out and see what happens
Markup is decided not by MA, not directly anyway, but by the players. It is up to ourselves to decide what the markup is. Sadly, undercutting to sell something is a very common behaviour among hunters, leading to lower markups.
Making certain drops more rare makes the markup to naturally increase.
There is a feedback mechanism in all of this. You get loot from mobs and minerals from mining, you decide how much markup should go with it, but then it is reflected in the gear that crafters create and sell back to hunters and miners. Thus higher MU on tools and weapons should trigger higher MU on minerals and hunting loot. But so far I've only seen this feedback to apply to mining, why is that? I think the answer may lay in mentality and behavior of an average hunter vs average miner.
Obviously on the other side of the coin we have the material requirements on blueprints that affect this as well.
Economy is a very fragile thing to play with and MA has a very unique opportunity to control most aspects of it (unlike governments in RL), but in the end its up to us what we do with it.
In the end there's a very basic idea behind MU called Supply and Demand.