There is no difference and economics does not distinguish between them.
Commodities are uniform goods that are interchangeable with each other. A good example is Oil, where one barrel is just as good as any other,
Intrinsic value is a complicated thing to understand, and in general there is no such thing. That being said certain specific subjects in economics and finance do have a more limited definition of “intrinsic value” that does exist. For example, a bank account has an intrinsic value equal to its balance (even though that balance itself may have no intrinsic value).
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