The reason salmon gives this message is because the Gencode transcripts have (for the purposes most people want to use them for) unnecessarily long and convoluted names. Specifically, there is the transcript id, and then a considerable amount of metadata encoded in the record name, separated by |. If you use these names for quantification, you end up with quantification files that contain these absurdly large names in each quant.sf file. In fact, because Gencode is such a common source of transcriptomes, Salmon supports special handling of Gencode transcriptomes where transcript record names are truncated at the first |. This means that in all of the quantification files generated via the index, the quant.sf files will just contain the transcript ids, and not the long names that are encoded in the input fasta file. Thus, unless you have a good reason not to, you can just pass --gencode to the index command to enable this functionality.