Hi VC,
We have never considered that the mzIdentML format might apply to Skyline. It is an interesting idea, but there is currently no support for exporting mzIdentML from Skyline. Though, we do support importing mzIdentML during a File > Import > Peptide Search or a Library Build. We have always considered it a format we import from other tools and not one that we export.
Sorry if this is a less-than-satisfying answer.
We always recommend that data processed with Skyline be presented to manuscript reviewers and readers through Panorama Public, which is part of the same ProteomeXchange consortium and satisfies the journal requirements we know of.
https://panoramaweb.org/Panorama Public/project-begin.view?pageId=Help
Hope this helps.
--Brendan