Should I store external API data in my WP database or keep it as a transient?

The way you are going about it is wrong. The source of data should not be relevant to how you store it in the DB. If the fact that this is a 3rd party service that supplies the data in some buzzword format confuses you, maybe you should try to imagine the input as coming from a low paid student doing a daily data input and how would you have built the DB then.

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