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It looks as though the air riveter used on the pop rivets removed the protective coating across most of the face of the aluminium rivet (it still seems to be visible on the edges). The riveter possibly had a worn nose piece on it, but the application of seam sealer should completely alleviate any corrosion issue from where the coating was removed.
As the SIB says, the structural integrity is due to the adhesive anyway, the rivets are there to tightly hold the assembly in place while the adhesive cures, the rivet corrosion without the seam sealer for surface protection would be more of a cosmetic issue in the future.
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