I have done baby quilts this way and they were fine. Granted, I only washed them once before giving them to the recipients, but that first wash didn't displace any batting. I would think since you're using a batting with scrim, and since the directions recommend a sewing distance of 8 to 10 inches, you should be just fine with the 3 you're doing. If there's some way you can elevate your sewing chair, perhaps with a cushion, that might help your neck, arms, and shoulders. Sitting at a higher orientation above the sewing machine bed may help some.