Unfortunately there does not appear to be a means to do this.
The default size is set as a result of you manipulating the size of your control is the designer. When you increase the width and/or height of a control the designer is interpreting your actions as a request to make the control that specified width and/or height.
A similar situation is encountered with the margins. As you alter the position of your control within the designer, it modifies properties to achieve the layout you've created. In the case of most containers the simplest solution is to modify margins in order to achieve the desired position, as you've already pointed out the simples solution is not always the most desired.
Personally I prefer to only use the XAML editor and only occasionally take a peak at the WPF Designer when I want to see the current layout. I also tend to favor using the Grid to layout most of my windows/controls as it provides the greatest flexibility not only for sizing and positioning, but for other tasks/features such as animations, transforms, etc.