Skyline does not really do anything like that, but we have plans to add some of those features in the future.
Another tool which some of the people in the MacCoss lab use is EncyclopeDIA:
https://bitbucket.org/searleb/encyclopedia/wiki/Home
EncyclopeDIA extracts chromatograms from datasets, and decides which transitions have interference based on whether they have the same shape as the other transitions in the same precursor, and whether the transitions have consistent behavior across the replicates.
If you do use EncyclopeDIA to create a .elib file, you can get it into Skyline by doing "File > Import > Peptide Search" and choose "Use Existing".
There is also the external tool "AvantGardeDIA" which I believe is supposed to also detect interference in transitions:
https://www.nature.com/articles/s41592-020-00986-4
-- Nick