Not generally - they can refuse a warranty service if it seems like the custom modification you made is causing whatever issue you're trying to use the warranty

Not generally - they can refuse a warranty service if it seems like the custom modification you made is causing whatever issue you're trying to use the warranty for, but they can't deny it if it unrelated. So if you have a warranty on your car, and you put a custom engine in it, and then it turns out you received defective seatbelts, the warranty is still active. But if your drive train is trashed from the extra power of the new engine, then the warranty will not be honored.