BMW's OEM nav system is considered by many who have it to be a piece of crap. The entire thing is controlled by the buttons and knobs which tends to make it tedious .. not like most other companies' nav systems that have touchscreens.
My whole setup cost less than the option and does more. Anyway, I dont know what route you were planning to take to fit a computer in with the OEM nav system, but it would be pretty difficult to replace the LCD .. it's a 6" screen by default w/o touch and it looks to be impossible to fit a 7" screen into the housing.
The best option that people are taking to use a car-pc while keeping the oem navigation is to get a hacked BMW TV Module that can display video while moving and hook a PC's TV-Out to the video module's aux input. The problem is that the hacked video module costs another $1000 and gets you NTSC video with still no touchscreen.
The other advantage to going with the nav system is that you can more easily keep the car's own CD player, radio, etc. There is an I-Bus based MP3 player also that integrates very well with the OEM system (I think by emulating a CD Changer or tape deck) .. displays song titles on the screen and everything .. that you can build in without even worrying about PC video.
Anyway, my only real piece of advice is that if you want the BMW nav system for some reason, don't attempt to retrofit it after you buy the car because it's very hard and costs over $4000 in parts alone to do. The main wiring harness is different with navigation.
Small other points about the nav system:
1) the radio tuner is in the trunk, thus the antenna cable runs to the trunk instead of to the front console.
2) There is a lot more reliance on I-Bus in a nav-equipped car. You will not be able to have a successful car-pc integration without building an I-Bus interface on a car with Navigation. Knowing how to program would also benefit you greatly.
All in all, I found that building my own screen mount and learning about BMW's electronics to be a very rewarding experience. I researched the BMW OEM navigation system extensively and was even planning a retrofit (I even own the current BMW navigation maps DVD!) before I decided to approach the PC route. Due to the high cost of new parts, I was scouring BMW salvage companies weekly to get ahold of a nav system. Everyone who has used the car-pc and either owns or has used a BMW navigation system says the PC is better.
My only complaint is boot times, and lack of a really slick software interface.. both of which I am currently addressing