As far as I can tell, the only way to do that is by calling the UpdateUserInventoryItemCustomData function multiple times, which can add up to your API limit calls pretty quickly.
I've circumvented the issue by breaking the server call into possible multiple calls so the API call limit is not reached. I wish there was a way to do that without having to do some workaround and possibly affecting user experience since the client might need to hang until all multiple calls are made.
Example: There are scenarios where the player might be rewarded with multiple items that are specific to a certain case. i.e. Chest gives multiple weapons, certain weapons contain enchantments based on location in which alter the stats for the given weapons.
tldr: "UpdateUserInventoryItensCustomData" function that allows multiple items to be modified in one API call.