To me, it looks like Encyclopedia is getting this right and Skyline is getting it wrong, just based on the first window, which both agree on without margins:
400.4319 to 424.4428
But adding the 0.2 margin, makes EncyclopeDIA start with:
400.232 to 424.243
Which seems totally reasonable, but Skyline uses:
401.2324 to 425.6433
So what exactly makes Skyline jump by 1.0005 before subtracting 0.2 for the margin? We will have to look into that. It is definitely intuitively obvious.
The two tools are obviously very close, except for this jump by 1 peptide optimized boundary m/z unit (1.0005). Initially I am guessing that Skyline is the one making a mistake, but it may turn out that there is some important consideration that underlies this shift, which didn't get carried from Skyline to EncyclopeDIA.