Transmutation explanation, please?

So I see that it's emphasized that transmutation turns runes into unnoted essence, emphasis on unnoted.

What's the trick, here? Go an altar and just eternally cycle?

Also, other than runes what's the benefits of Transmutation? Can I eventually turn copper ore into necrite ore for example?

I'm coming up to Tier 4, I need to choose a relic soon.

I have Endless Harvest, Animal Wrangler, Void Walker. Trying to figure out what to choose next