There were some new sounds added to the 20th anniversary cut that have actually made it into the mix now used for the theatrical cut but not all. Some of these fit, some dont. I’ll try to give a rough list of what they are. Might need some double clarification or elaboration on this.

A ‘bump’ noise added when E.T. rushes past the van when the Feds spot him, likely him bumping against the van’s grill as he rushes away. Now included in the theatrical cut.
Extra flash noises as the mothership flies by in the air. Now included in the theatrical cut.
E.T. hopping to his feet, followed by the fluttering away of non-existent birds, and the sound of E.T.'s feet as he advances toward the town. Now included in the theatrical cut, which makes no sense since these dont fit the action depicted in the original cut.
The word ‘shit’ is cut when Michael is at the fridge and sings the line ‘nothing but health shit’.
Extra ‘scream’ when E.T. is scared by the Tom and Jerry cartoon. Now included in the theatrical cut.
Mary tells Michael he’s not going out as a hippie instead of terrorist.
Alternate ADR added to the medical scene(s). The dialogue about E.T. having DNA is completely different and has new lines. The 2002 DVD of the theatrical cut has the original dialogue while the ‘new’ dialogue is included on the 2012 BD/DVD.
Radio static added to the scene where Mary and the feds approach the abandoned van. Included on the 2002 DVD of the theatrical cut but removed for the 2012 DVD/BD.