Firstly the wait is only a couple of months, and I would rather wait for what I truly wanted rather than compromise just so I could get close to what I wanted sooner. This is not a cheap car so I want what I want, I am not your typical Lexus buyer (if one really exists), but I think the IS250 is a very good car and represents good bang for your buck. If I am wrong then I can assure you that in 4 years when that time arrives I won't buy another Lexus unless the replacement is a good proposition.
I agree that resale could suffer however at my height the car would be traded a lot sooner if it had a moonroof as you would only hit your head so many times before you decided that you and the car should part company.
I did actually discuss this with the salesman and whilst most buyers would penalise you for not having a moonroof, some people don't actually like them (like me) and may in fact pay more for one that does not have one. I actually would have paid more not to have a moonroof, but instead received a reduced price for not having one. Now for the most important question (and if you can honestly answer this one I would also like this weeks tatslotto numbers) in 4 years when I plan to upgrade again and trade or sell my IS250 how much less will I receive for my car versus an identical one with a moonroof.