After some more testing i have found out that it seems to be strange handling in QTreeView::dragMoveEvent() function that causes the strange behavior. If i subclass QTreeView and make my own dragMoveEvent() function i can get the view and model to accept the disabled drop on the root item (while still allowing child items to be dropped on), but not otherwise. What i had to do was check the flags myself for each item being dragged over to make the drop function correctly.

Code needed: (beware, i dont claim this is complete... this is just a quick hack to verify my theory)

Qt Code: 
  1. void MyTreeView::dragMoveEvent(QDragMoveEvent *event) {
  2.     QModelIndex index = indexAt(event->pos());
  3.  
  4.     if (index.flags() & Qt::ItemIsDropEnabled) {
  5.         event->accept();
  6.     } else {
  7.         QTreeView::dragMoveEvent(event);
  8.     }
  9. }
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The culprit was these lines in the implementation in QAbstractItemView:

Qt Code: 
  1. ...
  2.         if (index.isValid() && d->showDropIndicator) {
  3. ...
  4.         } else {
  5.             d->dropIndicatorRect = QRect();
  6.             d->dropIndicatorPosition = OnViewport;
  7.             if (d->model->flags(rootIndex()) & Qt::ItemIsDropEnabled) {
  8.                 event->setDropAction(dropAction);
  9.                 event->accept(); // allow dropping in empty areas
  10.             }
  11.         }
  12. ...
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As i had drop indicator disabled (i draw my own) the code only checks the root items flags and thus it disables all drop indicators for the children as well. If i were to decide this would be a bug... the handling should be the same whether you want to draw your own drop indicators or not.

Below is the default implementation in QAbstractItemView:

Qt Code: 
  1. void QAbstractItemView::dragMoveEvent(QDragMoveEvent *event)
  2. {
  4.     if (dragDropMode() == InternalMove
  5.         && (event->source() != this || !(event->possibleActions() & Qt::MoveAction)))
  6.         return;
  7.  
  8.     // ignore by default
  9.     event->ignore();
  10.  
  11.     QModelIndex index = indexAt(event->pos());
  12.     if (!(event->source() == this && selectedIndexes().contains(index))
  13.         && d->canDecode(event)) {
  14.         Qt::DropAction dropAction = (d->model->supportedDropActions() & event->proposedAction())
  15.                                     ? event->proposedAction() : Qt::IgnoreAction;
  16.  
  17.         if (index.isValid() && d->showDropIndicator) {
  18.             QRect rect = visualRect(index);
  19.             d->dropIndicatorPosition = d->position(event->pos(), rect);
  20.             switch (d->dropIndicatorPosition) {
  21.             case AboveItem:
  22.                 if (d->model->flags(index.parent()) & Qt::ItemIsDropEnabled) {
  23.                     d->dropIndicatorRect = QRect(rect.left(), rect.top(), rect.width(), 0);
  24.                     event->setDropAction(dropAction);
  25.                     event->accept();
  26.                 } else {
  27.                     d->dropIndicatorRect = QRect();
  28.                 }
  29.                 break;
  30.             case BelowItem:
  31.                 if (d->model->flags(index.parent()) & Qt::ItemIsDropEnabled) {
  32.                     d->dropIndicatorRect = QRect(rect.left(), rect.bottom(), rect.width(), 0);
  33.                     event->setDropAction(dropAction);
  34.                     event->accept();
  35.                 } else {
  36.                     d->dropIndicatorRect = QRect();
  37.                 }
  38.                 break;
  39.             case OnItem:
  40.                 if (d->model->flags(index) & Qt::ItemIsDropEnabled) {
  41.                     d->dropIndicatorRect = rect;
  42.                     event->setDropAction(dropAction);
  43.                     event->accept();
  44.                 } else {
  45.                     d->dropIndicatorRect = QRect();
  46.                 }
  47.                 break;
  48.             case OnViewport:
  49.                 d->dropIndicatorRect = QRect();
  50.                 break;
  51.             }
  52.         } else {
  53.             d->dropIndicatorRect = QRect();
  54.             d->dropIndicatorPosition = OnViewport;
  55.             if (d->model->flags(rootIndex()) & Qt::ItemIsDropEnabled) {
  56.                 event->setDropAction(dropAction);
  57.                 event->accept(); // allow dropping in empty areas
  58.             }
  59.         }
  60.         d->viewport->update();
  61.     } // can decode
  62.  
  63.     if (d->shouldAutoScroll(event->pos()))
  64.         startAutoScroll();
  65. }
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