I’d fill the holes from the outside with jb weld and the silicone a patch of thin metal or plastic on the inside over the area. Should keep the rain out no problem.

This is sad to read... but since it's Friday, I will share a derogatory word for his type of shoddy work: "plumbtrician"... Sand a bit around the holes on the outside so the JB weld "holds". Don't fix anything if you plan to put the screws to the contractor.... as it were.