In this case is the best solution to measure distance between hole center points. Here is small (incomplete) example
HoleFeature singleHole1;
HoleFeature singleHole2;
HoleFeature multiHole;
HoleFeature holeByWorkPoint1;
Point centerPoint1;
Point centerPoint2;
//Two independent hole features
centerPoint1 = (singleHole1.HoleCenterPoints[1] as SketchPoint).Geometry3d;
centerPoint2 = (singleHole2.HoleCenterPoints[1] as SketchPoint).Geometry3d;
//Two holes in one feature
centerPoint1 = (multiHole.HoleCenterPoints[1] as SketchPoint).Geometry3d;
centerPoint2 = (multiHole.HoleCenterPoints[2] as SketchPoint).Geometry3d;
//Hole created by WorkPoint and axis
centerPoint1 = (holeByWorkPoint1.HoleCenterPoints[1] as WorkPoint).Point;
//Distance of holes
double distance = centerPoint1.DistanceTo(centerPoint2);