The price the 49ers have paid with all of their transparency is that we all know Shanahan and Lynch disagreed on Williams hours before he was selected. Peter King chronicled San Francisco's draft efforts back in April and we learned Shanahan pressured Lynch to put Williams back on the draft board, where he eventually drafted the Utah running back.
"Screw it," Lynch said to himself Saturday morning, via King. "I'm going to try to jump up and get this guy."
Four months later, the topic of Williams could become the first heated battle between a head coach and general manager who have been singing out of the same hymnal since their hiring in February.
If Williams was the undrafted signee and Matt Breida was the fourth-round pick, the 49ers would be releasing Williams this weekend -- without question.
Outside of a couple of flashes in practice and the preseason, Williams has been lagging behind. Breida was deemed so important, he didn't play in the preseason finale. Some 49ers assistant coaches were aware of how this storyline would play out way back in May.
Williams, on the other hand, fumbled twice against the Chargers on Thursday. He isn't a strong receiver. He hasn't been consistent. Couple that with the fact that Raheem Mostert is a special teams ace capable of making big plays and the evidence is just piling up against Williams. Lynch's initial thought process of keeping him off the draft board probably was the right play for the 49ers.
Lynch is not a vindictive person by any stretch of the imagination, but this is possibly the first time he can speak up and argue Shanahan was wrong on a player. Keeping Williams could mean the 49ers lose somebody such as Victor Bolden Jr., Adrian Colbert or Kendrick Bourne -- all rookies who have been entirely more productive than Williams in training camp and the preseason.
These are the tough conversations where egos have to be put aside. These are the types of conversations for which former GM Trent Baalke used to alienate staff members instead of collaborate. Other football players deserve to make San Francisco's roster over Williams. In front of the entire personnel department and coaching staff, is Lynch willing to convince his head coach this is the right course of action? Is Shanahan willing to admit his talent evaluation was wrong?
The question becomes if you keep Williams, will he even be active on game day? NFL rules limit the 49ers to dressing just 46 players each Sunday. If Williams spends his entire rookie season in street clothes, while Breida is thriving, the former Utah running back will essentially enter 2018 as a rookie. The new regime will bring in another rookie running back next season to compete. Williams' clock will be ticking.
I totally understand the argument to be patient with Williams. There are plenty of stories around the league of a player underwhelming during his first August and turning the corner his second season. This new 49ers regime probably won't want to completely give up on the second-ever offensive player it drafted. Injuries can also mount up at running back. Carlos Hyde is also a free agent after this season. It's never a bad idea to stockpile at this position.
But Shanahan has been a wizard with rookie running backs before. Alfred Morris and Isaiah Crowell each were setting franchise records in Washington and Cleveland. Why isn't it clicking for Williams yet? He also showed up out of shape during spring workouts – after Lynch had already red flagged his love for football.
The other problem is that two other mid-round draft picks are already considered long-term projects. Third-round cornerback Ahkello Witherspoon isn't ready for quality playing time. C.J. Beathard has looked fantastic for a rookie, but going against a real NFL defense will be a mighty challenge. Solomon Thomas, Reuben Foster and George Kittle will have large roles -- Williams was expected to be in that group when he was picked.
It had been reported that Lynch had final say on the NFL Draft and Shanahan had final say on the 53-man roster, but both men have reiterated every decision will be made together.
In particular, it's Shanahan who has long said he doesn't care about how much money a player earns, or where he was selected in the NFL Draft.
"It's about picking the best 53 football players," Shanahan said.
Can that mantra really be the case if the 49ers keep Joe Williams?