While I highly doubt GL cares one way or the other about the OOT anymore (I would certainly hope 4 Billion dollars was enough for him to get over his hang-ups about it), I would also think he'd want both versions out there in equal quality, or at least have the SE out there in higher quality.

That's why I don't think this new 4k job is for anything other than the SE.

Could they use it to restore the OOT as well? Maybe, but I'd hope in that scenario that they would know exactly what they're doing.