You are not wrong here Matt, this is the first time this has been brought up as far as I know.
(2) seems like the correct approach to me if you can swing it.
Otherwise I guess you will not have confidence the files are all there properly.
Once you get all the uploads into your S3 bucket is the general operation of Discourse OK? Are other changes needed for day to day use (thinking things like inventory may break - maybe changes are needed for pre-signed urls, etc…)