Any Custom League commissioner can edit the roster of every team in their league as long as the team manager has given the commissioner permission to do so. To provide commissioners greater flexibility when dealing with dormant teams, the option to allow or disallow commissioner control has been removed.
As a commissioner, you can edit another team's roster by going to your Commissioner Tools page and choosing the "Edit Rosters" option. Once there, select the team you want to alter and the type of transaction. You're then presented with options that allow you to make the desired moves.
Since you can only control one team at a time, you need to return to this page and follow the same procedure each time you wish to control another team.