Just goes to show that Cuben is no good for tarps.
Just kidding. For a lightweight, clean-looking (but not invisible), and permanent repair, I would recommend making a patch out of new cuben material (available from several online vendors, ie Quest Outfitters) and attaching it with Hysol U-09lv or U-09fl. I think this attachement method will give a much stronger and more tidy result than tape.
Just cut out the jagged edge around each hole, then cut two pieces of new material: a patch for one side and a patch with a cut-out for the other side:
If you clamp it well (or press it down with something heavy) while the glue is curing, it should give a neat-looking and permanent repair that is as strong as the original material with very little added weight. Tape would be a bit less labor, but it is likely to look less clean, and it won't be as strong.