A modification of the car will only affect the warranty if it can be shone that the mod. was a the cause of a
related failure or increased wear. If you paint the muffler and it rusts out in 6 months, BMW would probably claim that your mod. was the cause of the failure and not give you a new muffler. Since the BMW exhaust system is stainless steel and probably will last 8 or 10 years, painting it won't have any effect during the warranty period anyway.
Painting with the correct paint and performing the surface prep might actually enhance the life of the muffler. The muffler and exhaust tips do get fairly hot but probably not more than 400 or 450 deg. F. Way below what header paint or brake caliper paint is designed to take. However that's still too hot for plain acrylic enamel or powder coating.
Getting paint to stick to the stainless surface is the challenge. You must degrease (acetone works well on SS with pure ethanol as a second choice-Vodka in a pinch) and then lightly abrade the surface (steel wool) to have half a chance of getting the paint adhere properly. High temp. paint also tends to "fade" so you may need to repaint every 2-years or so unless you don't mind a gray muffler instead of a black one.
Here's a link to some
directions for muffler painting.