custom / targeted sequencing panel

[CynStr]

Hello,
I tried to find guidance on this online but was unsuccessful. I'm running an experiment using a custom oligo panel with my genes of interest, I've sequenced them using a MiSeq, and have already analyzed my data using salmon (mapping-based mode) using the following index:

grep "^>" <(gunzip -c GRCh38.primary_assembly.genome.fa.gz) | cut -d " " -f 1 > decoys.txt
sed -i -e 's/>//g' decoys.txt
cat gencode.v44.transcripts.fa.gz GRCh38.primary_assembly.genome.fa.gz > CRCH38_and_decoys.fa.gz
salmon index -t GRCH38_and_decoys.fa.gz -d decoys.txt -p 30 -i GRCh38_salmon_index --gencode

This index is for the full transcriptome and I then used tximport with a t2gene file containing only my genes of interest. However, should I have created an index containing only transcriptome data for my genes of interest? Would this decrease the likelihood of spurious mappings?

Thanks in advance for your response/help!