Because the custom node types introduced in the flow diagrams assembly are not simple shape nodes, you cannot create toolbox items for them using the ShapeTool.Shape attached property.

Creating Toolbox Items for Start, End and Decision Nodes

The flow diagrams assembly includes toolbox item resources for Start, End and Decision nodes which you can reference using the StaticResource element:

CopyA toolbox group for fixed flow diagram nodes
<ms:DiagramToolBoxGroup Header="Flow Control">
  <StaticResource ResourceKey="{x:Static ms:StandardFlowDiagramToolBoxItems.StartNodeToolKey}" />
  <StaticResource ResourceKey="{x:Static ms:StandardFlowDiagramToolBoxItems.DecisionNodeToolKey}" />
  <StaticResource ResourceKey="{x:Static ms:StandardFlowDiagramToolBoxItems.EndNodeToolKey}" />
</ms:DiagramToolBoxGroup>

Remember to merge the StandardFlowDiagramsToolBoxItems resource dictionary.
 

Creating Toolbox Items for Step Nodes

As a StepNode needs to be parameterised by a shape, there isn’t a singular tool resource you can use for step nodes. Instead, use the StepNodeTool.Shape attached property to configure a DiagramNodeTool to create step nodes.

CopyEvery diagram needs punched tape
<ms:DiagramToolBoxGroup Header="Step Nodes">
  <ms:DiagramNodeTool ms:StepNodeTool.Shape="Process" />
  <ms:DiagramNodeTool ms:StepNodeTool.Shape="Data" />
  <ms:DiagramNodeTool ms:StepNodeTool.Shape="Document" />
  <ms:DiagramNodeTool ms:StepNodeTool.Shape="PunchedTape" />
</ms:DiagramToolBoxGroup>