Skim is apparently safest to use (copying, e-mailing, etc.) when you save the pdf file as a PDF bundle, which includes the extra Skim data. In the Finder, a PDF bundle opens directly in Skim. I tried to drag such a PDF bundle into Scrivener and got an error (some parts could not be imported). Also the result appears as a normal folder, not something I can directly “open in external editor”.
Are each of these expected? If so, and since other programs also use bundle/package formats (e.g. Omnigraffle), might it be useful to support these in a future Scrivener?
I haven’t got Skim to test at the moment, but if it is saving as a “PDF bundle”, presumably this is something different to a standard PDF file that can be opened in Preview; presumably it is a file format specific to Skim. In which case, Scrivener will not support it.
And no, it would not be useful for Scrivener to support other package formats (e.g. OmniGraffle) as it would not be able to open them in its editor anyway. Scrivener cannot support every possible file type out there; that would be like asking it to contain every program out there!
2.0 will allow you to import files that aren’t supported directly by Scrivener, just for opening in an external editor, though; it should also do a better job of recognising package files and not interpreting them as a folder.