Hello!
Good questions.
- QIIME 2 can operate either on ASV or tables collapsed to taxa. Unless you specifically collapsed a table to a taxonomical level before biplot creation, in the process of creating a biplot with taxa names you should have received a biplot with individual feature hashes initially. Taxa are just labels added for the readability of the plot (instead of raw sequence).
- It is not possible to get loading scores for any type of PCoA, because it is not a linear dimensionality transformation technique. It is computed based on a distance matrix, and distance functions preserve no information about the features that make up the distances.
Here's a detailed explanation:
Using PCoA versus PCA - #3 by jwdebelius
Cheers
Valentyn