Good morning everyone

I am analysing the expression of some pseudogenes in my lab. However, the similarity between these genes and its pseudogenes are very high. Could this very nucleotide similarity influences the RNA-seq analysis? I am using HISAT2 software.
Since the HISAT2 software problably will align reads just to one position in the transcript annotations (may be align preferentially to gene copy and not for pseudogenes)?
I am trying to create a customized annotation with the 5’ends of each transcripts with carrying some degree of genetic variation (mutation accumulation and problably error from retroposition process)?
Could this strategy be better that analys the full transcripts?
If this stratagy could be a good idea, what would be better, to use this customized annotation at read aligment step or in the analysis of differential gene expression?