I've tagged a lot of features (c-stores in particular) on the building outline when I know the building has just one occupant. I will use nodes for shops/amenities if it's an obvious multi-tenant building, or even in the (now dwindling) number of e.g. Taco Bell/KFC/Pizza Hut multi-brand fast food outlets (actually, Dunkin and Baskin-Robbins are doing this). There are edge cases such as 7-Eleven and Laredo Taco Company where the latter is actually part of the former; those I've put on a separate node inside the 7-Eleven building.

I'm surprised Osmose actually throws this as a warning though. I have never seen it. I agree with "one feature, one element" in general, but taken to its extreme it would be to tag shop=convenience and amenity=fuel on the same node inside the fully enclosed building. That would make correctly tagging e.g. a 7-Eleven with Exxon fuel very challenging.