As you have noticed these 'properties' don't show up as properties, this is because they are built-in attributes, not properties managed by the prp file. However, to pass the settings from the symbol definition (the Inherit from Definition option) to the tools requires a property in the symbol editor - hence some inconsistency in what is displayed depending on the editor (symbols are ASCII so we need to embed the data somehow).
You should also take into consideration the 'Part List Exclude' property if you want such items to appear in the BOM but not on the PCB - this is discussed elsewhere on the community and also fully documented in the user guide.