Since this post has been revived I thought that I would add something interesting. When I first installed my boots about 2 years ago I also wasn't a huge fan of the fitment, it always seemed to me like the upper boot was a little too long and angled the wrong way. I always dreaded having to remove it from the MAF housing for any reason. Last weekend I replaced my motor mounts, raised my engine up about 1/2 to 3/4 of an inch, and now the silicon boots fit much better.
If Mishimoto engineered and test fit the boots on a car with good motor mounts, which I hope is the case, this would explain why some people are having fitment issues. If you motor mounts are compressed as much as mine were and the engine is sagging 1/2 to 3/4, the much less flexible silicon boots just aren't going to fit right. The OEM rubber boots with the accordion section will flex and stretch, the silicon will not.
Steve,
2004 330i zhp
2009 X3
2013 X1 35i M-Sport