Regarding AR, I agree with Laserdisc Master. I have past experience in that area and 720x480 is normal. The pixels are non-square but it doesn't make them wrong. To put the issue to rest, do a three way screenshot comparison between the blu-ray and your two methods and see which one overlays on top of the blu-ray better.

Regarding AA, like I said, you could do a mask of the area where the AA is obvious and just lose the detail in those specific spots in the frame. The detail is gone anyway if it is all jaggies. Of course that is a ton more work than just a script and is probably not worth the effort given the other projects going on in parallel.