Most of the things that need deleted as you've pointed out?
I've talked about years ago. I don't think the ship builders now days put that trash in. At least I hope not!
S3D can not be Autoit run to find and delete the stuff. Sadly it does not have the ability to be run that way. Trust me! I know!
A stand alone program could be done to scan and remove trash with a single pass of ALL files in a given folder and all sub folders.
I have a few scripts for 010 that do things like that but never wrote a full Trash remover script. Problem is not everyone will buy 010 so why bother?