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The green blocks represent inherited properties. The root type of the SWIS entity type hierarchy is System.Entity. It defines a few properties - DisplayName, Description, InstanceSiteId, InstanceType, and Uri - so all SWIS entity types will have those (because of how SWQL Studio builds that tree, an inherited property will have a blue block icon and be grouped with the non-inherited properties if the entity type has redeclared it for whatever reason).
The chain link icon marks Navigation Properties, which are a shortcut to a join. This can either be a simple foreign key join (like your StorageArrayID example) or a join through a mapping table for many-to-many relationships.
Thanks for the answer. It all makes sense now.