Addition to #3131, consider border when defining shape limits.

js/parts-3d/Column.js

@@ -30,7 +30,15 @@ wrap(seriesTypes.column.prototype, 'translate', function (proceed) {
 	var series = this,
 		chart = series.chart,
 		seriesOptions = series.options,
-		depth = seriesOptions.depth || 25;
+		depth = seriesOptions.depth || 25,
+		borderCrisp = series.borderWidth % 2 ? 0.5 : 0;
+
+	if (
+		(chart.inverted && !series.yAxis.reversed) ||
+		(!chart.inverted && series.yAxis.reversed)
+	) {
+		borderCrisp *= -1;
+	}
 
 	var stack = seriesOptions.stacking ? (seriesOptions.stack || 0) : series.index; // #4743
 	var z = stack * (depth + (seriesOptions.groupZPadding || 1));
@@ -44,23 +52,27 @@ wrap(seriesTypes.column.prototype, 'translate', function (proceed) {
 		if (point.y !== null) {
 			var shapeArgs = point.shapeArgs,
 				tooltipPos = point.tooltipPos,
-				dimensions = [['x', 'width'], ['y', 'height']]; // Array for final shapeArgs calculation.
+				// Array for final shapeArgs calculation.
 				// We are checking two dimensions (x and y).
+				dimensions = [['x', 'width'], ['y', 'height']],
+				borderlessBase; // crisped rects can have +/- 0.5 pixels offset
 
-				// #3131 We need to check if column shape arguments are inside plotArea.
-
+			// #3131 We need to check if column shape arguments are inside plotArea.
 			each(dimensions, function (d) {
+				borderlessBase = shapeArgs[d[0]] - borderCrisp;
 				if (
-					shapeArgs[d[0]] + shapeArgs[d[1]] < 0 || // End column position is smaller than axis start.
-					shapeArgs[d[0]] > series[d[0] + 'Axis'].len // Start column position is bigger than axis end.
-					) {
+					borderlessBase + shapeArgs[d[1]] < 0 || // End column position is smaller than axis start.
+					borderlessBase > series[d[0] + 'Axis'].len // Start column position is bigger than axis end.
+				) {
 					for (var key in shapeArgs) { // Set args to 0 if column is outside the chart.
 						shapeArgs[key] = 0;
 					}
-				} if (shapeArgs[d[0]] < 0) {
+				}
+				if (borderlessBase < 0) {
 					shapeArgs[d[1]] += shapeArgs[d[0]]; 
 					shapeArgs[d[0]] = 0;
-				} if (shapeArgs[d[0]] + shapeArgs[d[1]] > series[d[0] + 'Axis'].len) {
+				}
+				if (borderlessBase + shapeArgs[d[1]] > series[d[0] + 'Axis'].len) {
 					shapeArgs[d[1]] = series[d[0] + 'Axis'].len - shapeArgs[d[0]];
 				}
 			});