Welcome to the BMW family!
First, read this forum. All of the questions you've asked have been discussed extensively.
Pay attention to the model year of the vehicle - even though x3 from 2011 on are the same chassis (F25), options and engines change from year to year. What was standard changes from year to year. The composition of packages change from year to year. If someone tells you they got sport seats with the Sport Package on their 2013 X3, do not expect it to be true of the 2014 model year (there is no Sports Package in 2014 and the only way to get sports seats is to order the M-sport package).
Packages may change in the middle of the model year. The software on the car (whcih now controls many features may change in the middle of the model year. Chassis, trim, engines will not change in the middle of the model year. But they may change at the beginning. MY15 will see a Life Cycle Impulse or facelift change for the X3.Those cars start manufacture on 1 April 2014.
Learn the order sheet better than your salesperson. One is attached to the first post fo this forum. The latest I have seen is dated 1 May 2013. Your sales person should show you the latest sheet when you build your car. If they do not, go find another dealer. The sheet that is valid when you order your car is truth about the options available at that time. What was on the previous version of the order sheet or what was available last year have no relevance. When your salesperson enters the order they should print out the order form. As guyver626 said, it is a good practice to initial it, get a copy and then both you and your salesperson have a copy of what you agreed was on the order.
If you understand the order sheet you will have no surprises. The fact that you can only get paddle shifters as part of the M-sport package or that roof rails are optional are spelled out in the order sheet. If you rely on your salesperson to make sure there are no surprises, whether you are surprised or not will depend on how good your salesperson is. They vary from dealer to dealer and within dealerships.
The answers to most of your questions are highly subjective:
1. Depends on whether you stick with BMW service schedule or not. $0 for the first 4 yrs 50K mi if you stick with the BMW service schedule. If you are asking us whether you should stick to the BMW manint schedule, then that has been discussed extensively on all BMW forums. Religious issue.
If you are asking about lifetime maint cost, you'll get varying reports about how frequently BMWs break. But it is clear that BMW parts and labor are going to cost you more than those for a Toyota.
2. Depends on the dealership and your relationship with the people there. What dealer are you asking about?
3. It can depend on your car's build. Some '14 cars have had noise issues due to defective seals - read the forum for the details. Most, if not all, that I have seen reported here have been rectified. Beyond that, whether the X3, when built to spec, is "quiet" at 65 mph is highly subjective. A religious issue. Best answer - go drive one on the freeway. See what YOU think.
5. I don't have a phone that can do this, so I do not know.
7. (there was no 6?) Subjective. mugsy in the UK hates the ones he's seen. I have used a guy in Colorado Springs who I think does excellent work. I had one on my '05 Xe and loved it. I have one on my MY14 X3 and love it. No, I do not think it looks bad or is obvious. Yes, you can see it if you look hard. If anything starts to peel, my guy will stand behind is work and make it good. So it depends on your perspective and how good the person is who does the job. Your dealer is bound to have some on their lot that have them. See what YOU think. Look at Merc and Audi dealers and see what theirs look like. Find the best guy in your town and see what his work looks like.
8. Best advice I ever got about buying a car was to separate the car purchase from the car financing. Talk to the sales person about the cost of the car and the finance manager about the cost of the money. Doing that sends the signal that you will not put up with them trying to squeeze money out of you by trying to talk to you about payments rather than the total cost of the purchase.
I have dealt with both my credit union and BMW Finance on car purchases and found both to be good to work with.
9. Some people say yes and some say no. This is another topic that has had several threads.
Finally, download that order sheet and make sure you understand it. After you actually order the car, get a printout from the BMW order system and confirm that it is correct. Then get ready for all the fun you're going to have when you receive you X3!
Our BMW: '14 X3 35i, Deep Sea Blue, Black Nevada Leather, Fineline Wave Wood, Satin Aluminum Roof Rails, Premium Pkg, Cold Weather Pkg, Navigation System, Driver Assistance Pkg with ALL them cameras, Premium Sound
Our truck: '03 Ford F350, 7.3L turbo-diesel, 4WD, Lariat package, Lear topper, cow catcher, Blue over Grey (Go Rice!)
"Old Faithful's just a fountain compared to the glory of true love" -- John Prine