Keep in mind that Atkins is about losing weight & not about managing diabetes. This isn't to say that you can't do both on Atkins, but Dr. B's guidelines are more reasonable to me. The induction phase of no more than 20 grams for two weeks is pretty severe. By matching insulin correctly to carbs you shouldn't have lows.
The understanding behind Dr. B is to get your body used to eating a consistent amount of carbs & protein daily to fine tune insulin doses to prevent wild BG swings. Lowering carbs to 20 grams for a couple of weeks & then raising carbs later is a lot of changes to doses which isn't worth the trouble.
Also bear in mind that the other phases of Dr. Atkins allow for a good deal of protein that also effect BG.