The wiki says that if your dwarfs are wearing chain mail + high boots then you don't need leg armor like greaves. Does that mean that greaves are completely useless in such a situation, or does it still provide an armor bonus?
Secondly does wearing cloth underclothes or leather over clothes with metal armour provide any bonus to your protection? If so what are the best leather items I can combine with full metal armor besides hood and cloak?
You don't
need the leg armour because the boots and mail overlap. You still want it, because it's an extra layer of metal. It's similar to combining a mail shirt with a breastplate -- if you have the materials and your dwarves can still move quickly enough, why not?
Regular clothing items will provide a small bonus, but 1. It's unlikely that a blow will fall in the tiny gap between 'stopped by armour' and 'hits flesh', and 2. They're a pain in the butt to manage. Either you allow uniforms over civilian clothes and run the risk of dwarves choosing clothes over armour, or you make clothing items a part of the uniform and put up with dwarves complaining about the worn items they won't take off because said items are part of their uniform.
If you want your military to be uniformed in clothing, dress them in whatever you like except caps and shoes, but keep an eye on the dwarves' inventories to make sure they're still wearing their metal layers. Don't go by the green ticks in the military screen.