I'm sure others will chime in ...here's my 2 cents ..
I wouldn't try to compare Atkins to SBD...SBD focuses on unrefined /unprocessed whole foods. The focus is on SLOW carbs not Low carb. Slow meaning the effect of a food on your blood sugars. Frequent eating and slow carbs serve to steady your blood sugar levels -- not one with spikes and crashes that highly processed foods causes.
The focus is on healthy fats, no trans fats, low sat fats. Hence the limits on things like turkey bacon (that as you point out also has nitrates in it..)
The jury is out on eggs.. years ago eggs (the yolk primarily) was considered unhealthy and contributed to High LDL Cholesterol. Now I read that that is not necessarily true. I have eggs, and I have egg beaters...
I'm not sure I follow the bad fat analogy.. and agree that the SBD books and info are very unclear on what some of the terms like "Limited and Very Limited" mean-- and on portion sizes. I use the portion sizes listed in the Good Fats and Good Carbs guide as my guide. I also watch my calories.. cause although I am trying to eat "clean", I could easily eat tooo much of a good thing.
Some of us do combos of things.. WW with SBD eating, SBD and Calorie Counting, some do a modified phase 1 instead of full blown phase2. But SBD is a way of eating, a way of making healthy food choices for life.