Here's the raws I used.
Leather Leggings
[ITEM_PANTS:ITEM_PANTS_LEGGINGS]
[NAME:leggings:leggings]
[MATERIAL_PLACEHOLDER:leather]
[ARMORLEVEL:1]
[METAL_ARMOR_LEVELS]
[LBSTEP:MAX]
[LAYER:ARMOR]
[COVERAGE:100]
[LAYER_SIZE:15]
[LAYER_PERMIT:30]
[MATERIAL_SIZE:5]
[LEATHER]
Leather Boots
[ITEM_SHOES:ITEM_SHOES_LEATHER_BOOT]
[NAME:boot:boots]
[ARMORLEVEL:1]
[LAYER:ARMOR]
[COVERAGE:100]
[LAYER_SIZE:20]
[LAYER_PERMIT:50]
[MATERIAL_SIZE:1]
[LEATHER]
[HARD]
Modified Metal Boot
[ITEM_SHOES:ITEM_SHOES_FOOTPLATE]
[NAME:foot plate:foot plates]
[ARMORLEVEL:2]
[METAL_ARMOR_LEVELS]
[LAYER:OVER]
[SHAPED]
[COVERAGE:100]
[LAYER_SIZE:25]
[LAYER_PERMIT:10]
[MATERIAL_SIZE:1]
[METAL]
[HARD]
Modified Greaves
[ITEM_PANTS:ITEM_PANTS_TASSET]
[NAME:greaves:greaves]
[ARMORLEVEL:2]
[METAL_ARMOR_LEVELS]
[LBSTEP:1]
[LAYER:OVER]
[COVERAGE:50]
[LAYER_SIZE:10]
[LAYER_PERMIT:20]
[MATERIAL_SIZE:3]
[HARD]
[METAL]
Entity
[SHOES:ITEM_SHOES_FOOTPLATE:FORCED]
[SHOES:ITEM_SHOES_LEATHER_BOOT:FORCED]
[PANTS:ITEM_PANTS_LEGGINGS:FORCED]
[PANTS:ITEM_PANTS_TASSET:FORCED]
dwarves who are wearing armor will consider themselves 'naked'
Really? Have you tried using metal leggins? That works for me.
Double Really? Perhaps you aren't waiting long enough, I believe the clothes need to fully rot off and a few months need to pass, this can take multiple ingame years.
If you're right, it's probably that leggings have the [LEATHER] tag. So the game is treating it as metal clothing/armor hybrid thing.