Well, you were right to be worried, and apparently the government was too. The Magnuson-Moss Warranty Act applies to car warranties for everyone. Of course, the warranty can still be voided if you are irresponsibly cavalier about your vehicle, and aftermarket parts could still cause your warranty to be voided; however, keep in mind that if you have everything in order, the warranty provider, whether manufacturer, dealer, or independent, cannot simply wave off a warranty claim.
All service and maintenance records should be retained; any quality brand parts can be used in place of the originals. While you do not need to use OEM manufacturer products, the service receipts should contain details like the odometer reading, model of vehicle, identification number, and date; the brand names for different products should be included as well.
There are frequent concerns that cosmetic work on a car can void a warranty. In the vast majority of cases, this is false. Unless the cosmetic work done actually affects the normal mechanical operations of the car somehow, it will not void a warranty.
The same is true for aftermarket auto parts. If you install an aftermarket auto part and another component of your car breaks down, the dealer has to prove that that aftermarket part was responsible for the original parts' malfunction before it can void your warranty. Bear in mind, however, that if the aftermarket auto part breaks down in your car, your warranty will not cover it.
Regardless of federal statutes, if the warranty states clearly and conspicuously what terms will void a warranty, the warranty will still be voided if those terms are fulfilled. This means if your warranty explicitly forbids aftermarket parts installation or cosmetic changes, then any actions that fall under those categories can void the warranty. Some states have additional statutes that protect consumers.
The Owner's Manual that comes along with the car will contain a section listing everything you should not do. Obviously, you should service the car regularly as recommended by the Manual. If you somehow still find yourself in a sticky situation where you believe the warranty company is trying to rip you off, then you can report them to the Federal Trade Commission. More information is available at their website.