It looks like you want to have one row per Replicate, and have each Molecule in a separate column.
Skyline makes it easy to create a report that goes the other way: one row per Molecule and the Replicates in separate columns. There is a checkbox at the bottom of the "View Editor" which is "Pivot Replicate Name", which does that.
You can make it so that the different molecules appear in different columns using the Pivot Editor.
To do that, you would add the following columns to your report:
Replicates > Files > File Name
Replicates > Sample ID (assuming you have defined a Replicate Annotation called "Sample ID").
Protein > Peptides > Molecule Name
Protein > Peptides > Peptide Results > Quantification > Normalized Area
Then, when you are looking at the results in the Document Grid, press the "Group/Total" button (it's next to the Views dropdown).
In the Pivot Editor, add the following columns as Row Headers:
File Name
Sample ID
Add the following column as Column Header:
Molecule Name
And, choose "Mean" in the dropdown and add Normalized Area as a Value.
You can find more information about the Pivot Editor here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PivotEditor
-- Nick