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I have a team of 4, do they all have to submit a game/only join to get a certificate?

The name that will be written in the contents of the charter certificate is the username of the sender's itch.io account, so it will not affect whether you are working as a group or individually because what you will see is the sender's itch.io username. If each person (4 members of your team) sends the same game with a different itch.io account, you can be reminded that the name of the game sender with the itch.io username will be included in the charter. but is it permissible for 4 different itch.io accounts to take part in 1 game jam and submit the same 1 game?

Maybe you misunderstood from what i meant to be. Just in case if you don't know in itch.io you can add multiple publisher at the same game. So will it automatically make a seperate certificate for each member of the publisher?

No. It can be reminded again, for now the policy is "the sender of the game will be written in the charter". If you really want this then we will reconsider