Two types of connectivity are defined within the Connectivity Model: logical and physical. Physical connectivity is an actual physical connection between two physical items. Logical connectivity is a connection, typically shown graphically, in which at least one of the two items is not a physical item.
One example of a logical connection is a P&ID pipe run connecting to an equipment nozzle. Although the nozzle is a physical item, the pipe run is not physical; it's a logical representation that results in a set of physical piping items (pipes, elbows, bend, and so forth). Likewise, Smart 3D runs, although routed in the 3D space, are logical rather than physical (you cannot touch them, but you can touch the components that are generated based on them).
Since a run is non-physical, all connectivity relationships definitions involving runs are logical.