EvanShultz comment hit the nail on the head:
Is there a way to short nets, global or not, in such a way that the
location of the short on the PCB can be chosen by the user?I am not sure how dangerous this would be but may be the tool should support NET_SHORT property such that it can be applied to nets and when done so, the tool will allow two differently named nets to be connected without giving Line to Line spacing error. Of couse, utmost precaution will be required...
I think v16.3 added jumper support but not sure if that applies in this situation.