Obviously Jordan would be a terribly tough matchup to defend, but Thompson, Iguodala, and Durant are about as good a trio as you would find, the more interesting question to me is who is guarding Curry, Thompson, and Durant? Can Jordan keep up with Curry? If not, that means someone like Ron Harper or ironically Steve Kerr is guarding Curry, good luck with that. If Jordan can stick on Curry, then Thompson gets the mismatch with Harper or Kerr. Also, I have doubts that Pippen has the speed to stay with Durant. Durant is a special kind of athlete that there just weren't many of in the 90's.
I can't think of a single team the Bulls played that would force both Pippen and Jordan to play both ends of the floor all game long (the Sonics were probably the closest with Payton, Hawkins, and Schrempf). Almost all of their opponents in the Finals and entire Eastern playoffs really only had 1 tough wing/guard matchup, so Jordan and Pippen could swap off defensively saving them more for offense and even Rodman would get in on the defense for the bigger wings on occasion.
I'd be surprised if the Warriors didn't win under either set of rules (assuming they were still bombing 3's) because they would just be too hard for the Bulls to defend, especially on the perimeter, and unlike some of the other teams of that era, the Bulls had no one down low that could create a mismatch. I mean it isn't like Shaq, Ewing, Robinson, Hakeem, etc. was playing for the Bulls. Even a guy like Karl Malone would cause so many issues for the Warriors under the older rules. The Bulls just don't have that player on either 3 peat as Ho Grant was the best they had to offer down low.