Should not need to modify them 
It would still store it in there as /uploads/ etc for the S3 bucket or uploads/
The provider and format I think is internally for Strapi to use, or info itself not how it’s rendered.
Strapi itself will prefix the URL with the backend etc, unless you want to extend files using cloud URL
I had to rewrite at work to use cloudurl when this was enabled. But for normal Uploads for S3 it should work just fine.