Are the data sources for Waffles and the Chrome visualizer different? It sounds like Waffles is real-time and the Chrome visualizer is not real-time. Do they use the same macros and route the buffer differently? Or do they have entirely different systems for gathering the profile data?
Waffles is more than just a profiler. It is a nice, high level interface into our (non-public) debugging API. You are correct that the profiling info there is real-time, while Chrome is post. They all use the same buffers, but just interpret the data a little differently.
There is also other profile info which is gathered by Waffles, stuff like number of visible particles, texture calls, GPU cost per emitter, amongst others, and that information is gathered through another interface.