What a dirty messy job..So what do you think, Before

After
I cant believe there is no underseal at the back of the car its just finished in grey paint. Most of the rust is just surface thankfully apart from the box sections where the rear beam attaches. After cleaning at all back and striping all the surface rust away these holes are now two great big holes!! not sure how to repair these to be honest..
I’ve now hit white stonechip sealant now should I remove this or just clean all the muck of it?