If it were me personally, I would never 'compromise' per se on a car which costs $50k. I'd want it EXACTLY the way I like it. But then again that's just my personal take on it.
It really depends on your situation, and more importantly your NEEDS. If you absolutely need the car within the next week, month etc. then only go ahead and compromise and buy one off the lot. As far as the $1k holiday rebate goes, you'd get that irrespective of when you take delivery, all your CA needs to do is lock you in to the program.
And I absolutely understand the agony of waiting for your car, but the end reward will be much pleasant as you'll be getting the car specifically built for you.
335i ///M-Sport Mineral Gray | Black-kidney Grilles | Performance Exhaust