That does seem a little odd to me.
I’ve checked, and the source file is spot on. I’ve just looked at it in our design software, and the box is set to be exactly 1 inch by 1 inch. And I printed the same page you have, and mine measures exactly to spec. I’m not sure why you’re having the issue you are seeing. It could be due to the printer and/or printer driver you are using.
One thing to check: are you opening and printing the file with Adobe Reader? Some other PDF readers are known to not handle printing to scale as well.
The measurement is made from the outside edge of the line to the outside edge of the line. Try measuring that and see how much closer it gets you. From the look of your photo, I’m guessing you may still be a hair off. Chances are that amount won’t make a difference in your sewing. But if you want to be completely accurate, you could scale the document to 101% or 102% to get the measurement from outside edge of line to outside edge of line to be exactly one inch on your printer. I’ve heard from someone before who did this and it worked fine.