Hi Lasse,
I'm not sure how the communication settings work with the auto upgrade feature of SEPM. I would assume that on the next heartbeat the client would perform the upgrade based on how many clients are performing their upgrades now. I apologize but I don't know where to verify how many connections the SEPM can handle at once by default.
In my opinion, let it run for an hour see how many clients upgraded. In my experience, the clients upgrade failry quick for those that are online.