Primarchs may fly directly to any destination which is connected to its current location by an unbroken series of friendly hops. If you can draw a line from your Primarch’s location to its destination without crossing an enemy castle, then that is the path the Primarch will choose to take.
Travel time is a maximum of about 10 minutes for Primarch travel.
Once a move order has been issued, you cannot cancel or change your movement. This means no more waypoints––the Primarch must complete its previous order before the next one can be issued.
Attacking Mines and Poachers now only require being in the same Region as the target, and no longer need the Primarch to travel to them.
Generally, it’s safest to hop from Safe Zone to Safe Zone to avoid getting trapped in a region with no escape.