What is the difference between transparent and non-transparent entities?

Non-Transparent: Entity claiming tax refund entitlement; has paid the tax to be recovered. Documentation is only needed at the entity level. Examples include charities, individuals, and IRAs. 

Transparent: Underlying investors have paid the tax to be recovered and can claim the entitlement. Documentation must be gathered at the beneficial owner/investor level. Examples include partnerships, master-feeder funds, LLCs, and trusts.