The 99 THX color timing is not how it looked in theaters. Cundy had stated they could not possibly afford to photo-chemically time it the way they wanted. It was a very very low budget film. So the 99 DVD was a "what-if" release.
And frankly, I think it works far better that way. I was so distracted by the first BD being overly summery green I couldn't enjoy it.
For me, the older color timing is king and I wonder if it is possible to alter the current BD to match. I am thinking it would take some serious work. Far beyond what I am capable of. :(