Eh indeed that is contradictory. I guess, in my mind I was thinking "well, I don't mind using some other approach, as long as I can use NCBI so that all info retrieved is consistent". Now, given the problems that I've found, I guess "consistency" is not the best word to describe NCBI's FTP..
The idea of using Uniprot is ok for retrieving the proteins. I am now trying to see if there is an easy way to retrieve their genomic sequences because this is the big problem that I am facing now.
Also, I added a snippet of the kind of output that I would like to get.