Smoking in PG-13 films -- including background shots and other passing instances -- was just as strongly linked with real-world experimentation as the smoking in R-rated films.
This could create incentives for game developers to PG-13-ify their releases in much the same way NC-17 ratings have placed a ceiling on the kind of content we can see at the theatre.
As for the rest of the franchise, Indiana Jones and the Temple of Doom was never a great sequel (although the fourth film made it look brilliant), but it was revolutionary in opening up the PG-13 rating.
Scenes of smoking have become increasingly rare in non-R-rated movies, according to the MPAA. Of the movies portraying smoking in recent years, 72% were rated R, 21% were rated PG-13, and 6% were rated PG.