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Surely the aerodynamics of both would be very similar?
Not really, a covered spoked wheel has to flare out to at least the flange spacing of the base hub, whereas as true disc can be whatever width the designer chooses all the way from hub to rim. Also, it's harder to make the profile continuous from flange to bead if you're adding covers to a spoked wheel. The differences are in the area of small marginal gains, and dependent on what frame is feeding air onto the disc.
What are the benefits of a real disc wheel over a regular wheel with covers? Surely the aerodynamics of both would be very similar?