I think it is a clear indication that the gene was expressed in that particular genome, isn't it?
No, I disagree. Strictly speaking the way you quantified is incorrect and does not allow your conclusion. As Rob pointed out, you didn't use Salmon correctly, and the way you used it has two potential problems:
1) if you map to only one gene, reads that would otherwise map perfectly to other (similar in sequence, but different) genes and not map to this gene, may now may map to this gene;
2) if this gene has high similarity with other genes, reads would map to multiple locations, but their quantification could be ascertained accurately due to Salmon EM algorithm. Now, in the absence of these similar genes, you may be over-estimating the counts.
Use Salmon as intended: quantify the reads against the whole set of transcripts from your species, then examine the counts and TPM for th gene of interest.