Thanks for the reply!
The mesh I have will always intersect, how does asking absolute distance helps?
This sign computation also gets unstable on points that are not so far from other model.
The model I shared looks easy to force sign above certain threshold, there are models which blends together (like a woven rope).
Just curious, If this is unstable how does the Boolean operations succeed? (https://www.vtkjournal.org/browse/publication/797)