He would struggle with a lot of the new breed of fighter, but he would never struggle with Conor. Not ever. He wouldn't struggle with a fighter who was choked out by Nate Diaz, and only managed to win a majority decision in the rematch. BJ has fought far more lethal, skilled and powerful strikers than Conor, and Conor has literally no other ways to win. Conor's only chance would be to try and kick his way to a decision and hope he doesn't get tired out, and good luck with THAT, BJ has great take downs. He took down Jon Fitch. He can take down Conor... And if that fight hits the mat, just how much of a chance do you think he has? You can talk all you want about Conor's "under rated grappling" but don't play that game when we're talking about BJ Penn.
I'm not some old timer stuck in the past. BJ has a better chin than Diaz, so good luck knocking him out (he had never even been wobbled until very late in his career). Fast hands, great head movement, and according to GSP the fastest reaction time he has ever seen. He's a nightmare for Conor.
Khabib, on the other hand, would probably be a nightmare for BJ. He actually has all the tools. Conor has one hand.