You'll need a new flute every time you want to cast Voice of the Mountain with the bonus in Power Level granted by using an Ingredient, yes.
Using an Ingredient is optional.
exactly, this helps balance the power of the spells, even though it is more fiddly bits to take account of. One thing my players are starting to do is research new spells. I help them understand the appropriate level and power of the spell, but then I take a close look at spells of this type and level to be sure there is a spell component that is of similar value and rarity to keep the spell more balanced. I don't let variants that have no components even at less power be developed, as that goes against the spirit of the system.
It does make for some interesting role-play, looking for regular claws on a mutant animal almost ends in frustration. Having a stack of severed hands in your backpack is a little hard to explain to the warden.