GMs and scouts get paid a lot of money, and spend a ton of time, analyzing players......particularly QBs. So as fun as it is to criticize them, presumably they have a pretty good idea of what they're doing. So it's amusing to hear fans spout off about how player X is so much better than player Y, as if their opinion is gospel.
That being said, to your point, it's still a bit of a crapshoot.
But I do think there's something to looking at QBs who didn't play for championship caliber teams and throw for eleventy billion yards. Look at the SC QBs after Carson Palmer. Until Kessler, they all hard absurd talent around them. When your O-line can dominate the opponents' D-line, and your WR's are wide open on every play, it's easy to look like a stud. I think the guys who played on more average teams stand a better shot in the NFL. Like Goff, for example, is used to being under pressure, used to being hit, used to having to fit a ball into a tight window because his WR's weren't world-beaters, etc., etc.
That doesn't mean he, or Wentz, is a guarantee by any means. But I feel like guys of that mold are better equipped to deal with NFL conditions.