My personal take is that icons should conform to the squircle, but have a permitted amount of break out from the core shape. For example, Audio Hijack’s icon as presented in the article should be allowed to have the microphone extend past the border slightly. The squircle should be mandated as the core shape, but with just tad bit of flexibility and shape definition.

This keeps grids feeling proper, organised, and aligned, without feeling like the icons of Android Honeycomb.