Ha! We've spent a lot of time talking about this on several forums (and other vehicle forums have extensive threads devoted to this very topic). The opinions are, as you might imagine, either for or against them.
Like any mechanical device there have been problems. And if you're familiar with internet forums you know that problems are multiplied x 1,000 compared to no problems (for the most part, no one talks about not having problems and how good the sunroof is while one person with one problem with a sunroof can make it sound like it's the end of the world).
Ford obviously has lots of experience with sunroofs on and offroad and has confidence that theirs won't cause problems. Heck, they made the Raptor a SuperCab body style unlike the Lightning which was a standard cab. Putting "suicide doors" on the Raptor is a much greater challenge than a sunroof (the SuperCab design has no pillar for the front door to latch into - it latches into the rear, suicide door). On a truck like the Raptor, designed for high-speed offroading, the SuperCab design is a winner - Ford did their homework, did the engineering and they have lots of experience making that design work. Something to consider: some years back GM/Chevy came out with their Extended Cab pickups and their first versions had, if I recall correctly, a fixed panel behind the driver - the only back door that opened was on the passenger side).
In any case, the Raptor flat out works with the sunroof. I don't open mine all that often but I enjoy it when I do and I really enjoy being able to slide back the sunshade and let the light in through the tinted glass roof. Being able to open the sunroof up when I want and letting sun in is worth it to me.
In my opinion, knowing what I know now about this truck, I would not wait another day if I were you. I'd go to the dealer and get the truck as long as it has what you want in it. I'd jump and click my heels knowing that I don't have to wait another day to get in and drive my brand new Raptor.
I hope you'll give it serious consideration. Just think of all the days you'll miss if you keep waiting just to avoid getting a sunroof!