The first account to log in to Destiny 2 gets assigned the season pass. Based off your post it sounds like you signed in to Steam first and found cross save wasn't active. Unfortunately that means the season pass was unlocked on the underlying Steam D2 account and not your later cross saved account.
Currently there is no process to transfer in-game content between platform accounts.
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How was I supposed to avoid that? I quit the game when I saw the warning about the cross saves, set it up, and I still had this happen. There has to be something that can be done to fix this.