Hi @ahale004,
RE 1: RESCRIPt does not currently provide tools to directly download pre-formatted BLAST databases, e.g. ('nt'), which are located here ftp://ftp.ncbi.nih.gov/blast/db/. Using the full pre-formatted nt database would be much quicker than downloading and compiling yourself. You can, read up on how to run BLAST locally.
One of the other devs reminded me that we have been considering adding this feature to RESCRIPt via these relevant GitHub PRs:
But we do not yet have a time-line for when we'll be able to implement this. Until then, I'd recommend a making several amplicon-specific reference databases. More on this below....
RE 2: As far as I know, it is not possible to download the nucleotide BLAST database via a query.
RE 3: There are many ways to generate reference reads for use in qiime feature-classifier classify-consensus-blast, all you require is a way to construct a taxonomy.qza and a sequence.qza file. Some examples of which are here.
Making individual custom databases:
Have you read through the RESCRIPt tutorials as listed here? There are several ways by which you can use RESCRIPt to make specific custom amplicon databases using data from GenBank. For example, there is one tutorial for making a trnL database, and another tutorial that outlines a different approach, on constructing a 12S rRNA gene database.
-Cheers!