You can easily make a barebones disc, using only:
DVD Decrypter
PGC Demux
AVISynth + DGMPGDec
CCE
Muxman
After that, it's not much extra work to modify the GOUT disc using VobBlanker to swap out the original video with the video from your new anamorphic disc; the existing menu structure of the GOUT disc is kept intact.
It starts to get a bit more complicated if you want to remove things like the lego preview and THX optimizer.