I think what is happening is Goff is not good enough to overcome poor RB play and only having two wideouts who are threats.
Queue up the 9er game. Receivers are blanketed on many snaps. They miss having that third heat that can eat up the opposing CB3 which means teams can single-high us and even zero when the front is good enough.
And the RBs. Those guys are lost man. They line up wrong. They miss holes. They get dinged up. They run the wrong routes and turn what should be a perfectly drawn up play vs the right look from a big gainer to a mediocre gain. It's not good. Brown is only good running the ball between the tackles but he's out there to not screw up when he's lined up outside, but he does screw it up. Hendy has no idea what he's doing half the time, Goff telling him where to line up.
Goff simply isn't good enough to overcome those things. He's a good QB just not great. And he might be at his ceiling, but we have to wait and see.