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There is no a best option to deal with this case, whatever you use Expeditionpcb or Allegro. A common method is use special drill symbol and add notes in fab drawing ,tell pcb fabs to route those slot holes. Not like Allegro which allows to define mutiple holes for padstack, Expeditionpcb doesn't allow it. However, In Expeditionpcb, you have two options:
Option# 1: define a rectangle hole(punch) for the padstack, add a note like "all punched holes should be routed..." in fab drawing. You get the benifit, however, your pcb fabs have to prepare the route data. Due to Expeditonpcb seperately output those puched holes, so it's easy to prepare the route data.
Option #2: define a normal hole(drill) for the padstack. At last stage of work, you add rectangle contour around the padstack. You pcb fabs will get benifits becaue Expeditiopcb will automatically output the route data