As far as I'm aware what you call S3 profile is actually an AWS API Access key. And since in the credentials, there is a type called AWS credentials, I think it would be much better to store the Access key ID and the Secret Access key there, since if you are using S3 there is a pretty high probability, you are using other AWS services too.

Also, from a jenkins user perspective, if I want to store any kind of login/password pair, authentication credential or secret, I would do it in the "central" place which was created to do it, instead of putting it to the system config.