I think the problem is a conceptual one.
The purpose of a circuit board is to join things that are not otherwise connected. If you tell the tool A,B,C need to be connected, then the tool assumes that there needs to be copper track connecting A,B,C on the circuit board.
If in fact, you are telling the tool that A,B,C are already connected then no tracks need be created, and in fact there is no need for any copper tracks at all, perhaps just some mounting holes. (e,g A and B might be legs on a component which are internally connected, A and C will be connected by a wire jumper, B and C are separately connected to a telephone exchange which links the two together).
There are some rare cases where it might be desirable to make use of "hidden" connections, but equally there are many cases where you must have all the pins connected, e.g. GND pins on an IC are internally connected, but you must connect them all on the PCB. Rather than add complexity to the tool to try to describe all the possibilities, it's a lot easier to use some human intelligence. You know what you are doing better than the computer does!