@Nathan_Hubot, I'm going to leave the main part of your question to others.
I think you'll be happy to know, however, that some common diversity metrics can now accept FeatureTable[RelativeFrequency] data without any manipulation required. Specifically, any measures used in core-metrics-phylogenetic except for bray_curtis allow this. qiime diversity alpha, beta, alpha-phylogenetic, and beta-phylogenetic should let you run those calculations.