I don't know much about the science behind the coffee question, but I can tell you this.
My sister has been on Atkin's for over a year now and has continued to drink black regular coffee (non-decaf) the whole time. She has had great results with this WOL and has never said she's had a problem with any of the items you have spoke of.

Just figured I list this info for ya-all.

Cheers, John

PS: I dropped coffee for the first 6-months completly. I currently have 1-2 cups a week now. Only when I really feel like having one.