Transcriptome vs genome reference in gene expression analysis

Question

[bioinfo1994]

Hello. I have paired-end mRNA sequencing data with an average read length of 75 bp. My end goal is to analyze gene expression and perform variant calling to identify SNVs. I would appreciate your guidance on when to use a genome reference and when to use a transcriptome reference (with a splice-aware aligner) for these two tasks and in general, along with the reasoning behind each choice. Thank you so much!