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Most of (probably all) "Preferences\Papyrus\Diagram\PapyrusUMLSequenceDiagram Diagram" and "Properties for project\Papyrus\Diagrams" options are not taken care of. Changing its values doesn't reflect in setting new default values in neither existing nor new projects or diagrams. One of the most disturbing options is "Element icon" which is unchecked by default, yet is always treated as if it checked. (OMG UML spec "17.8.1 Sequence Diagram Notation" does not requre to use any element icons.)
These options were supposed to be removed for all elements in all diagrams, but we forgot to remove the main page of each diagram. The preference pages have been replaced with CSS/Theme capabilities. It is the standard Papyrus Theme which provides the element icons for all elements