Notice those are flanged holes. The flanges stiffen the part. The parts may have been designed to rely on the stiffening effect and a flat sheet without the flanged holes may very well buckle below required demand. Adding a hole to what is specified as a solid sheet could cause the same issue, all depends on the loads it must take and how the piece was designed. Now the door frame mentioned above, doesn’t take flight loads, so putting holes in it isn’t a big deal, but a spar or other critical component I’d stick to what the designer specified.