Did you try moving the custom padstack origin different in custom padstack editor such that traces wont cross the pad. For any change on the origin of custom padstack, you may need to go back and check the cell also in cell editor.
Changing the custom padstack origin is indeed a solution but it means that the coordinates of the padstack shape have to be changed and this can be source of errors in some cases.
Another example is when you have staggered pads (cf image below). It would be very easy to make such a cell if you could have the pad origin outside the copper area because then, the pads are aligned along the green line and you just have to rotate one every two pads to get what you need. Because of the trace connecting to the padstack origin, you need to create a standard pad and then, staggered the pads manually by calculating the coordinates. It is not an impossible task but I just wanted to know if there was a clever way of doing it.