Not a bug, but could be done better. Currently there's not enough information saved for the fleets to use the coordinate of a pickup area relative to the ship the drone is directly docked to. It still uses that coordinate though, but then relative to the mothership.
Instead it might be better to just use the coordinate relative to the main ship, which I think is also the suggestion of the OP. This has as downside that it would not work for pickup blocks on moving rails.
Best solution is to actually use the UID of the ship that currently is used for the pickup point coordinate, which is the entity with the used pickup block on it.