Before I retired I worked building sun roofs for a company that supplies all the Big 3 plus all the major foreign brands.

  The sunroof frames even those huge sunroofs are designed to replace the structural strength when you cut out the steel roof.
 
99% of the leaking issues are related to the rubber seals, the rest in some mfg defect that wasn't caught.

I wouldn't worry about a roof mounted rack system.
  Your talking about around #100 plus pounds spread over 4 contact points on the outer edge of roof which is the strongest part. You didn't mention if your pick-up has side rails? Just make sure you get a rack made for rails or no rails.

This is a top of the line rack but you get the idea.

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Something a lot cheaper.

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Or something like this.

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