ETS2: Set waypoint when picking up cargo
Solution 1:
If you accepted a job from the pause menu's Freight Market, the GPS should automatically be pointing to the pick up point. (The button even say "Set as GPS Destination".) You can also add waypoints to your way, if you want to make detours, but the endpoint should always be the pick up.
However, if you accept a job from a business directly (through the floating green question mark, all you get is a green flag on your GPS and a bouncing arrow above the cargo to be picked up. You can't even put in a waypoint on the map.
However, this method should never take you to the other side of Europe. In stead, jobs accepted at a business should always be the pick up point in itself, so there should be no need for a waypoint, unless you decide to take a drive around the block.
As to how you managed it, either there was a bug in the game or you misunderstood something.