S T R U C T O R I Z E R - User Guide
Settings > Boxed diagram?

This setting influences the way the diagram is drawn. Boxed diagrams are somewhat larger because there is a special box drawn around the inner elements. Non-boxed diagrams are reduced in size, obviously.

The heading of an un-boxed diagram is gray whereas the box around a boxed diagram is white:

program, boxed  program, un-boxed 
Boxed diagram  Un-boxed diagram 

For further details about this, please look here...

Whether diagrams are presented in boxed or un-boxed style has no impact on execution or code export.