I would implement custom delegate where I would draw checkboxes with QStyle or QStylePainter and implement clicking on it in QAbstractItemDelegate::editorEvent(). I would not implement highlight on mouse hover, because it will be more complicated and is not necessary. Of course check state of those checkboxes would be stored in model, not necessarily in Qt::CheckStateRole only as there are 2 checkboxes. And then I would use this delegate only in this one column where it is needed so I wouldn't have to take care about other columns in delegate while implementing it.
That's my idea :]
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