Differences between github and published protocol: Which are the correct modes in step 3?

[LXsasse]

Hi, I am trying to follow this protocol step by step to estimate changes in degradation rates, and while it says on here to use "-m intersection-strict" for exons and "-m union" for introns, it says to use "-m intersection-strict" for both in your protocol "Analysis of mRNA Dynamics Using RNA Sequencing Data" (https://link.springer.com/protocol/10.1007/978-1-0716-2409-8_9). I am even more confused because it says in the protocol that "The number of reads assigned to the pre-mRNA and mature mRNA of a gene is the union of reads that overlap the gene’s intronic and exonic regions, respectively", but then "-m intersection-strict" is used for both below.
Could you please clarify which one is correct?
All the best,
Alex