In ArcGIS Pro 1.3 & 1.3.1 the Intersect gp tool does not produce any valid output if the first input feature class contains a near vertical polyline ZM and the second input feature class contains a Polygon Z.
If I choose the ‘Point’ at the output type the resulting output feature class remains always empty. However the intersection is clearly visible: see attachment below. According to the visual examination the result should be a single point.
Ákos Halmai