Yep, that's a valid concern.
I personally think switching the system, having a 21 y.o. player play in the biggest spotlight in sports, and making them the leader of 52 grown adults at the start of their careers presents confounding variables to the argument that it's just the system change that's affecting these players. Even spread QBs have to go through their progressions and accurately deliver passes under pressure. Calling all spreads the same is painting with a wide brush.
Aaron Rodgers was the original spread system QB under Jeff Tedford who had groomed former NFL first round busts Derek Carr, Joey Harrington and Akili Smith (all of whom started immediately, missed large portions of training camp, etc.). This brought about concerns about whether Rodgers was a product of the Tedford system or a legitimate NFL prospect. My point is, yes, system should factor into the equation, but only as much as it pertains to the prospects ability to play the position. I don't think the system is making him more accurate or protecting him from having to make passes under duress that would inflate his numbers nobody is going to make the argument he is the most athletic QB in this class.
Also, something that never gets brought up, there was no rushing offense for Cal during Goff's tenure, and we've all seen how much that can improve a QB's play. The highest rank the team achieved was 87/125 BCS teams. So teams new Cal was going to throw and just couldn't do much about it.