Let the RenderFlowThread layer have an empty size.

Source/core/rendering/RenderLayer.cpp

 /*
  * Copyright (C) 2006, 2007, 2008, 2009, 2010, 2011, 2012 Apple Inc. All rights reserved.
  *
  * Portions are Copyright (C) 1998 Netscape Communications Corporation.
  *
  * Other contributors:
  *   Robert O'Callahan <roc+@cs.cmu.edu>
  *   David Baron <dbaron@fas.harvard.edu>
  *   Christian Biesinger <cbiesinger@web.de>
  *   Randall Jesup <rjesup@wgate.com>
@@ skipping 3129 matching lines @@
         ancestorLayer = this;
 
     // FIXME: This could be improved to do a check like hasVisibleNonCompositingDescendantLayers() (bug 92580).
     if (this != ancestorLayer && !hasVisibleContent() && !hasVisibleDescendant())
         return LayoutRect();
 
     // The root layer is always just the size of the document.
     if (isRootLayer())
         return m_renderer->view()->unscaledDocumentRect();
 
+    // The layer created for the RenderFlowThread is just a helper for painting and hit-testing,
+    // and should not contribute to the bounding box. The RenderMultiColumnSets will contribute
+    // the correct size for the rendered content of the multicol container.
+    if (useRegionBasedColumns() && renderer()->isRenderFlowThread())
+        return LayoutRect();
+
     const bool shouldIncludeTransform = paintsWithTransform(PaintBehaviorNormal) || (options == ApplyBoundsChickenEggHacks && transform());
 
     LayoutRect localClipRect = clipper().localClipRect();
     if (localClipRect != PaintInfo::infiniteRect()) {
         if (shouldIncludeTransform)
             localClipRect = transform()->mapRect(localClipRect);
 
         LayoutPoint delta;
         convertToLayerCoords(ancestorLayer, delta);
         localClipRect.moveBy(delta);
@@ skipping 536 matching lines @@
     }
 }
 
 void showLayerTree(const blink::RenderObject* renderer)
 {
     if (!renderer)
         return;
     showLayerTree(renderer->enclosingLayer());
 }
 #endif