Can commissioners set the keepers for another team?

To specify the keepers for a single owner, go to League » Settings » Set Keepers and select the team. From there you can select keepers just as you would for one of your teams.

To specify just the keepers for all teams, you can go to League » Settings » Edit Rosters » These are the keepers only. This will set the players on every team and mark all of them as keepers.