OP, the M3 is my first manual car as well, and while I don't really have anything to compare it to, it does indeed seem that there's a lot of unnecessary pedal travel.
However, I've found as others have mentioned that seating position can have a HUGE impact on your shifting ability/smoothness. Try playing with your seating position, remembering that you can slide the steering wheel back and forward as well in case that becomes an issue. I tried about 4 different seating positions each for at least a couple weeks before I settled on the one I have, and I sit noticeably closer and LOWER in this car than I probably would if it didn't have a clutch (or than I do in my wife's AT car). The lower is so that I can push the clutch in with more of a forward motion rather than a "down and forward" motion.
You can indeed burn out your clutch by riding it even slightly. The reason is that there's little to no dead travel at the BEGINNING of the clutch, but there's a lot toward the END. That means that you could theoretically shift cleanly without pressing the clutch pedal all the way down (hence the clutch stop), but I wouldn't recommend trying this unless you actually had a clutch stop because if you don't have that marker of how far you need to go, you risk not going far enough and causing at best excess wear and at worst some real damage.
Good luck and enjoy the M3 and learning stick, I've found both very fun and rewarding!