So, i solved it. You have to pretty much set it up exactly like you would set up a multi-stage PLR, you can't really save some entities there.
So, all you need to do to get the prefab to work correctly is the follwoing:
1. Add a team_control_point_round, name it something like "plr_singlestage". Priority 1. Control points this round: "cp_blu cp_red".
2. After you did this, the "Team" settings of info_player_teamspawn wont work anymore. So you also have to change "Blue Spawn for round" to "plr_singlestage" for the blue spawns and "Red Spawn for round" for red.
You're done, now single stage PLR works as intended.
This problem really costed me countless hours, i am so happy that i solved it.