I think what you're posing makes total sense - in an ideal world. Sadly... we don't like in an ideal world and taxonomy and phylogeny don't always line up. I talked about it here a while ago (featuring and emojis).
We also have a second issue: that taxonomy annotation isn't perfect. (I'm going to send you off to read Nick's excellent discussion here)
But, essentially the problem boils down to the fact that taxonomy ≠ phylogeny and you can't collapse your data and have it map to your tree.
So, you can run non-phylogenetic metrics on your data, but phylogenetic metrics require a tree. Which needs OTU or ASV level resolution.
and 
emojis).