Neat! The Youtube channel Noodle recently did a related deep dive into the differences in the releases of The Matrix [0]. The back half of the video also touches on the art of transferring from film/video to digital.
Another movie with the same / similar problem is the DVD release of the Lord of the Rings Extended editions. Both Blu-ray and 4K version. As far as I remember is that they fixed it for the theatrical version in 4K but not extended.