...then what I get is a single .tar archive, itself containing several hundred thousand .tar archives - each of those containing the text file with the FASTA nucleotide sequence. It would require 2-3 days for my modest but capable Mac Core Duo to untar all these archives and I expect a further day or two for it to cat them into a single flat text file.
So, how can I download a single flat text file (or a manageable number of text files, e.g. 10 files) of the entire NCBI prokaryote Genbank and Refseq databases as nucleotide FASTA?
Unzip and convert from annotated Genbank (.gbk) format to .fna format using any of a range of tools.
It is surprising to me that this is not as straightforward for prokaryotes as it could be. As I mentioned in my original question, on the NCBI Virus web interface, whole-database nucleotide FASTAs (RefSeq and Genbank) can be downloaded as a single nucleotide text file with a single click. I have queried this with NCBI and will update this answer if they can add anything to this.
To the best of my knowledge, what you want to do is not possible. I don't know the exact reason, but I would guess it is because there isn't enough demand among users to download a single flat file with all RefSeq genomes. Most people like to customize their downloads, and most people have no problem (g)unzipping and concatenating thousands of files.
The recipe you show above for flat .fna files is most likely incorrect, possibly because you are not pointing at correct directory. It is easy to show using genome_updater that there are 17439 RefSeq bacterial genomes that fulfill the "Complete Genome" criterion (as of June 8th). Likewise, there are 357 RefSeq archaeal genomes fulfilling the same criterion (as of right now). If you do the same exercise but extend this to RefSeq genomes that are not complete (considered in "Contig" state with a reasonably small number of contigs), there are additional 97100 genomes among bacteria (as of June 8th), and another 459 among archaea (as of right now). These numbers are considerably different from what you have.