Trey had multiple chances to keep his job and become the QB of the future for that team, so I wouldn't use him as the example of your argument. He was ass then and still ass now.They had plans for McCarthy to be their QB until he got injured. It's a very similar situation where they have 2 QBs to be actually concerned about. Geno's situation didn't have the Seahawks draft a top 10 QB draft pick to be concerned they just had Drew Lock to be concerned about. The Bucs didn't have any other QBs to be concerned about either when they offered Baker his contract.
McCarthy's people ain't going to be happy to just have him sit there and wait for him to play IF Darnold fukks up.....and keeping them both creates a looking over the shoulder situation IF Darnold fukks up. They can't keep both and have everyone be cool about it. The 49ers tried it with Trey and Jimmy G and it blew up......then later with Trey and Purdy then it blew up.
Darnold is playing at too high of a level this season, so you have to ride it out as long as you can regardless of how McCarthy and his team feels about it. This situation isn't as difficult as you're making it out to be.