I allow myself two cups of coffee on a full stomach (after breakfast and lunch, for example). I've never had a problem with my stomach except for that period during which I snacked on chocolate-covered expresso beans.
My SWAMI diet is a blend of BTD and GTD Explorer, but I'm not totally compliant. Also I try to choose foods that have a Low Glycemic index. DW and DD are A+, probably also Explorer.
Thanks for posting S.Peg... Coffee (even regular) still doesn't seem to be affecting me either & I have to say my skin is staying clearer (not sure if there is any connection, but who knows, there could be?)