I think most fans would agree to any release of the OOT, even if they had to buy Jake Lloyd to get it.
Although I understand your point, this doesn’t sound reasonable. The SE is the official version as far as Disney and LFL are concerned. They are not going to release a box set with the OOT in place of the SE. It would either be a separate issue, or it would be bonus discs like the last time.
Of course, it’s extremely unlikely to happen at all, unless people pressure Disney to do so.