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I think you underestimate just how crap leather and bone are for protective purposes in-game.
You could have asked instead of making assumptions about my assumptions.
Leather armor isn't worth making in the slightest IMO, and bone, while it may protect from some weaker and smaller creatures, breaks very easily (even breastplates and greaves). Chain leggings and mail shirts do help definitely (particularly against edged attacks), and iron ones definitely aren't worse than bone stuff of any kind.
Leather armour satisfies citizens' need for modesty, doesn't degrade over time, doesn't require metal, isn't excessively heavy, and can be an additional layer that reduces momentum by a few percentage points (assuming the Material Science entry on the wiki is correct). On its own, I consider it an attractive alternative to civilian clothing, not a replacement for metal armour.
Leather armour over mail shirt should offer the same protection as 2 mail shirts.
Bone greaves should offer the same or better protection than metal leggings when worn over mail shirt and metal boots.
In either case, the advantage over a single metal layer is marginal, and civilian clothing would do just as much.
Leather armour alone would be much weaker than a mail shirt, same for bone vs. metal legwear. That hasn't come up here, probably because it's obvious.
...well-trained soldiers with this sort of "medium" set up can usually overpower armed opponents before they can get a good hit in at their otherwise-exposed legs.
That said if werecreatures make an appearance I'd always recommend leggings get prioritized as a bare minimum addition to that, because even copper chain armor is going to be better than literally anything made of bone or leather at stopping bites from things like that reliably, at which point you're once again making a compromise of trading weight/encumbrance for better protection.
Which exposed legs, though? Mail shirt + high boots leave no gap, and by the mechanics it hardly matters if you wear chain leggings of the same material on top or an elf-made ramie skirt - a layer is a layer.
If the leggings stop an attack that the skirt doesn't, the attack doesn't get through the boots/shirt anyway.
In fact, if the mechanics in the wiki are correct, we have slightly bizarre behaviour that makes leggings and mail shirts especially unsuitable for layering:
Weapon success against a layer reduces the attack momentum by a few percentage points.
Weapon failure against a layer permanently converts edged damage to blunt, but doesn't change momentum for flexible armour (leather by elasticity, metal leggings and mail shirts by token).
Additional strong layers may do less to degrade blunt hits than additional weak layers.