The problem is the journalism, the article writing - it's misleading and lacks facts. All of these magazines are trying to sell a story, "autoblog picks 1M over M3", "335is competes with M3" - I promise you that these articles are written to get attention. To draw people to read, I'm sure the 1M is a great package, I'm sure it represents the M division well. All of these articles promote debates about who is faster, which is the better package. The journalists want to stir it up, they want people to say Holy **** the 1M is better than the M3. I wouldn't be surprised if some magazines fudge track #s for sales purposes.
If you wanted a dual duty track and commuter car, I'd say that the M3 has a bigger trunk, more space, offers a 4-door option, EDC and DCT. But if you wanted to save 15-20k, the 1M makes a great runner-up.