Wow, that is a beautiful quilt!!!! The shadowing and being a bit "off" from the others is part of being handmade. Only God and a machine are perfect.
I am by no means a perfect sewer not quilter. My sister is the perfect one. Its my imperfections that she actually appreciates as just part of me. I'm uncomfortable with my errors too, but I get over it. If I didn't, I'd dislike the process.
Ok, that being said, I guess if it bothers you that much you can pull out the stitching. I think the quilt is beautiful and the "imperfections" make it special - handmade.