My guess is that you have one of those "Liability" factory triggers, somewhere between 9 and 11 pounds of pull, which would be more than 75% of your problem.
I have a .308 Featherweight that had just about the same problem when new 20 yrs ago, some things never change. I had two holes about an inch apart or less and one flyer, always one flyer out of 3 which did give me a 3 to 3 1/2 inch group. The stock was making contact with the barrel about half way down and the trigger was lightened to 2 1/2 to 3 pounds. My rifle now clips holes at 100 yds. Slide a dollar bill down between the stock and barrel after 3 to 5 shots and see if you get any tight spots, if you do the harmonics change enough to throw your shots off at 100 yds. And being a Featherweight, it isnt too advisable to be shooting it so quickly that the barrel overheats.
You have a good rifle, it's just that Winchester factory standards don't usually comply with what the end user expects. You'd think that if Savage can do it with mass produced rifles - Winchester could do it also, but I guess not. If you did send it back Winchester would most likely would do nothing but tell you that it meets industry standards. But it may not hurt to call and find out for sure.
Before anyone might say that I single out Winchester, I do not. Other makers have the same problem also.... It's called Quality Control.