I would still put the hand holes in like v1. Then make a 'plug' for each hole with a thinner top layer about 1/2" bigger than the holes. So you have a cover for each with a plug inside to keep the cover from moving around. Then drill your mounting holes in those plugs rather than the deck. The drill holes, being small, will be hard to seal. So you move those the the plugs which are easier to replace.
What about some small rubber blocks on the bottom of your metal cross bars sitting on top of the factory front to back bars in the roof, that way some of the weight will be transferred to the original support and should prevent any flexing.
Also make an air deflector for the front, look at the roof rack on a nissan xterra how it has that bog flat plate laying back at 45degrees on the front. Make something like that and curve the bottom to match the roof then mount just behind the sunroof.
What about some small rubber blocks on the bottom of your metal cross bars sitting on top of the factory front to back bars in the roof, that way some of the weight will be transferred to the original support and should prevent any flexing.
Also make an air deflector for the front, look at the roof rack on a nissan xterra how it has that bog flat plate laying back at 45degrees on the front. Make something like that and curve the bottom to match the roof then mount just behind the sunroof.