This seems to be a known problem, eg: http://forum.arduino.cc/index.php?topic=197083.0
But I do not like the advice given in that thread (unsoldering the SPI connector).
I found a simple solution, just bend the three pins not available on shield (ICSP.1, .3 and .4) with a nipper to a degree of 45 degrees. That allows plug connection that stays below the proto shield:
I needed the SPI pins to connect a ILI9341 320x240 display. The border of the display does not allow to use a connector directly besides the display connector, therefore I made one connector a bit sloped with two little spacers:
3.3V was available once, but needed for LED and VCC of display. For that the 5x1 connector on the left side was added.
Finally I added two 3x8 connectors for a motor controller.
This is the connected and working result (Arduebot with ILI9341_due library "graphicstest" running):
The display on Arduebot will be used for PID controller constants determination while Arduebot is trying to drive fast parallel to a dentless long wall..
For me bending 3 pins seems to be less invasive than unsoldering the whole connector, and easier to revert.