Chad, I'm certainly not in the same league with the folks on the MBB videos, but I've always "sighted" down my arrow shaft. I don't conciously "gap" but I certainly take the windage out of the equation with my arrow shaft/point. After that, it's just the elevation to get right. As long as I do my job on alignment and release, it goes right where it should.
If memory serves, I think Rod and Larry both shoot 3-fingers under, which gets the arrow up higher, and closer to their eye. I have a lower anchor point, and shoot split fingers, so like you, I tend to cant my bow some to get the arrow right under my eye. I shoot with both eyes open, and focused on my "spot". (I believe this is commonly referred to as "split-vision" but I just call it "what works for me"...)
By squinting with your left eye, you may be messing up some visual references, or distorting your sight picture enough to cause the "right" misses.
Good luck, and good shooting!
Curtis