Just because Lucas added some changes in special editions, it does not mean the whole thing became a different film, and it certainly does not mean that Fox suddenly did not own the rights any more. So if Fox opposed re-release of the film, then there would be no special editions either. It is a simple logic.

For Fox, it was a win-win situation whatever Lucas wanted to re-release, because it was Lucasfilm who had to spend money and produce the re-releases, while Fox basically just profited with almost no effort. If Lucas was willing to spend money and restore the original version, Fox would without doubt happily welcome the “free” profit.