A lot (if not all) of the FX shots were recomposited. It's no secret that GL kept all of the film elements, they made a very big deal out of that when the SEs came out in 1997. I watched a documentary or 2 that talked about how most film-makers from that era didn't keep the separate film elements, and just kept the finished composites. The reason that they were able to go back and re-composite everything for the SEs was because GL had made sure not to discard the separate film elements, which was unusual at the time (and very smart, on his part).
So, all of this crap about there not being suitable material for new OOT transfers is just that - crap.