Oh! Are you feeling that Skyline-daily is not aware of the other modifications that are listed when you use Skyline?
The imported search results appear to contain the modifications listed below.
Please select the ones you wish to add to the document.
Of these 6, I believe the first is only defined (by your or in some way imported) in Skyline and not Skyline-daily. And the last behaves the same in both Skyline and Skyline-daily.
The middle 4 then are already included in your Skyline-daily document, which is why Skyline-daily is not asking you about adding them. This is borne out by Pic4.
I expect that if you show the same forms in Skyline as you did for Skyline-daily in Pic4 that you will find those 4 modifications are not checked in the Peptide Settings - Modifications tab, which is why Skyline is asking you about adding them to your document.
Sorry, that is so confusing. I guess we can think about improving the wording?
"The imported search results contain modifications not found in your document.
Please select the ones you wish to add to the document."
Would that have made more sense? Skyline doesn't bother telling you about the ones already explained by your document settings.
I hope this finally gets to the point of your question. Thanks for the screenshots.