Try zooming in on the spectrum graph you have in the PowerPoint slide. I expect you will find that it is a profile spectrum. Skyline sums the signal found within your extraction range with profile data, you should find that if you are zoomed in enough to see the multiple peaks in the spectrum that if you add up the ones highlighted by the colored band, that they add up to the point shown in the chromatogram.
We actually have made no effort to make Skyline produce numbers on the same scale as Xcalibur. However, you should find that if you do a linear regression between their numbers and ours that they correspond very closely. Our numbers have been used a great deal and vetted in many papers. We are confident they produce valid quantitative results comparable to instrument vendor software, as claimed in this paper from the Hoofnagle lab:
But, our peak area numbers do not necessarily match vendor peak area numbers. Though, they should be quantitatively consistent.
Thanks for posting to the Skyline support board with screenshots of what you are seeing.