I just did some tests, and making the LD's into an 'anamorphic' version really does kill the quality.
I think the reason is two fold.
1) The resize - by resizing the available video without black bars to 720x480, there is some quality loss (though not much)
2) The encoding - this is where it really makes a difference if you are using pro encoding tools. The quality of the encode is much lower, due to the fact that you are encoding full frame 720x480, you end up with a lower quality encode, vs encoding the 4:3 black bar version, where you are effectively not encoding the pixels that make up the "black bar space".
So you are forced to use much higher compression --but not getting any more detail--
It is really noticeable on Jedi, where luke gets out of his x-wing after crash landing. On the anamorphic sets you get a lot of MPEG pixel issues in the fine detail of the xwing. When going with a 4:3 encode, the bitrate is high enough to make them go away.
So it looks like my first version is going to stick to the original format/ratio of the Definitive laserdiscs. I may then do an anamorphic later as it will still look a lot better than the current version due to going dual layer and effectively halving the compression.