How to get the longest fasta sequence including all possible switching isoforms of a gene out of isoforms
From your question it isn't clear if you are trying to identify the isoforms that have a very high or very low differential expression value, or if you are trying to correctly find an orthlog for your top hits using BLAST. 

If your question is about isoform-level quantification, identifying DE at the isoform level is challenging and DESeq2 is only designed for gene-level analyses. That is why it is only outputting genes rather than a specific isoform.