"what I cant understand is how/why SG does not process the documents for metadata while pulling all the documents through it."
I presume you mean “pushing” the documents through it?
As I indicated earlier, pre CB5.0/ SG 1.5, if you want to making an existing bucket available for mobile consumption, you need bucket shadowing but that is going away.
So a suggestion is to instead of restoring a bucket with the docs that you need to sync, start with an empty bucket (or restore bucket to only include docs that you don’t want to sync) and do a bulk push of the docs through sync GW using admin REST API.
Again, do you have the option of mobile to SG 1.5/ CB 5.0? If so, then this will work seamlessly for you