The 0.01 m value is hard coded for collinear points (https://github.com/NREL/EnergyPlus/blob/develop/src/EnergyPlus/SurfaceGeometry.cc#L6414). There Seems like the engineering reference is a difference between the minimum precision (1 mm) with which geometry is modeled and the minimum distance between two vertices. The idea is that the resolution out of geometry modeling calculations should be a bit finer than the resolution you can enter for geometry on input. The Engineering reference could be clearer but it is talking about resolution and doesn't actually say what the collinear check is, that is in the warning message.date.