I think you know how that is scored. Gurley gets 0.9 points and Goff get 1.1 points or Higbee get 1.1 points in your second scenario. Sure, it seems a little unfair, but 3rd and 1 is a tough yard to get (I think we both know he's not running a QB sneak on 2nd and 1). Also, it is far much more likely that Gurley rushed twice for 4.5 yards each than a single 9 yard run. That's not bad, but I don't think two 4.5 yard runs really deserves an extra point.
But your stated scenario is much more rare than a 3rd down back catching a meaningless dump off for 7 yards on 3rd and 10 and getting 1.7 points. 
Goff had two rushing first downs last year. Duke caught 74 passes last year. Only 34 went for 1st downs. Meanwhile, Gurley had 69 rushing first downs and 31 receiving first downs. In the long run, PPFD rewards the players that are picking up the tough yards and moving the chains. However, PPR is blind. All receptions are worth the same. If a guy catches a pass and gets tackled for a loss, he gets more points than the player that wisely intentionally bats the ball down to save yards and clock. If a guy catches a 7 yard pass on 3rd and 15, that's worth the same as catching a 7 yard pass on 3rd and 5. But we all know the defense was willing to give away the yard catch on 3rd and 15 uncontested, while the 7 yard pass on 3rd and 5 was likely highly contested. These should have different values!
Landry is a player whose value I feel is inflated by PPR. In the past 4 years the guy has 401 receptions. Only 221 have been for first downs. Mike Evans only has 309 receptions, but 245 of them have been first downs. Evans has 959.4 points to Landry's 937.1 - barely 5 points per season more, despite having 10 more TDs than Landry, over 500 more yards, and 24 more first downs. That's crazy. Change it to PPFD and we're looking at 895.4 to 757.1. Seems much more reasonable, IMO.