discarding dovetail mappings

[igordot]

From Salmon 0.13.1 release notes:

This version adds the --allowDovetail flag which overrides the newly-default behavior of discarding dovetail mappings of paired-end reads. If passed this flag, salmon will not consider dovetailing mappings as discordant, and will consider them.

I am trying to understand why the default behavior is to discard dovetail mappings. In my personal experience, most of the dovetail mappings are due to short fragments, so both mates of the pair end up completely overlapping. In that case, I would think that dovetailed reads should be retained. Are there are other factors that contribute to discarding dovetails by default?

[yeodynasty]

Any idea? This is interesting.