Currently tracking beacons for are based at some height (depending on the type of beacon) extend into the sky. When they are set to pulse the pulse begins at this base height and moves upwards.
The requested changes should help with locating what is being tracked more easily:
1) Have the beacon start at a height of 0 with a blue color extending to the base height
2) Have the beacon use a red color above the base height extending to 5,020 meters (the unassisted flying height limit)
3) Have the beacon pulse (this is controlled by the CheesyBeacon debug setting), with the direction of the pulse in the direction of what is being tracked. Thus there will be a pulse moving upwards from the ground and a pulse moving downwards from the sky.