How do I efficiently perform a metagenome screen of “all” species?
As you point out, BLAST is not going to work well for reads from a typical RNASeq experiment.

From an RNASeq dataset, you might be able to get away with just a ribosomal screen using Silva, because the ribosome is the most abundantly transcribed gene. This will usually be the case even if polyA selection or ribosomal depletion was carried out on a sample.

However, bear in mind that there will be a lot of false results due to database incompleteness. I used Kraken when I did something like this a few years ago, and ended up with one sequence annotated as a fruit bat (where my subject was a water-living planarian flatworm). Centrifuge would be a better option now; the authors even claim that they can store the entirety of nr in a 70 GB index with Centrifuge (which would be better / more comprehensive than just a ribosomal screen).