It has everything to do with scouting. Teams take the wrong shots all the time for reasons that make no damn sense. There were teams that didn't like Marcus Mariota last year because of the system he played in. The same this year with Jared Goff. They blame spread schemes for their inability to scout. All of this 'pro-style' bollocks that gets spouted seems to disregard that the majority of teams run spread concepts in the NFL and the majority of snaps are from the shotgun.
There are guys that go undrafted every year that have more talent than some of the guys that go on the first 2 days of the draft. They just simply don't tick the right boxes.
Sean Mannion was a 3rd round pick last year. Chris Bonner spent 2 days with KC in a rookie minicamp and then ended up in the CFL for a while. I know which one was better, it just so happened that playing poorly in the PAC-12 meant more than dominating D2. If you don't draft the talent, you end up in a QB crisis. The NFL has made it for themselves.