I see 2 downsides.
1. If Ben gets hurt and misses a few games, Rudolf comes in and lights it up and then begins the incessant talk of having a QB controversy for years to come. Not a terrible problem to have but could become a distraction.
2. We picked Ben's replacement a couple years too early and Ben doesn't retire until Rudolf's rookie contract expires and we have to overpay to retain an unproven backup expected to fill Ben's shoes or risk losing him to someone else willing to pony up the money. See the Pats situation with Garoppolo.
To me, it seems like a risk willing to take and the insurance only cost a 3rd and 7th round pick.
I just think back to Ben's 5 picks against the Jags early in the season and how many fans would be calling for Rudolf to start if Ben does that again this season. Despite the horrible game, Ben still went on to have one of his best statistical seasons and was the only reason we were remotely close in the playoff game against the Jags. So as a fan who tries to have a level head about things, it will be frustrating to see fans calling for Rudolf when Ben throws some head scratching picks (because it WILL happen). Which IMO is what Ben is more worried about than actually losing his job to Rudolf. The QB transition distraction is inevitable but if Ben is planning on playing 3-5 more years, is it worth starting the distraction now? Only time will tell but you can't blame the team for planning for the future.