There are multiple ways to set-up External Storage mounts:
You can set-up them globally (what it sounds like you did)[1]
You can mount them at the user level[2]
You can use variables for user mountpoints[3]
Also, another option, if you’re only using S3 for all your data (and you also aren’t in need of accessing it from outside of Nextcloud) is to simply use S3 as Primary (not External) Storage[4]. Then it behaves the same as a local drive. It becomes your datadirectory basically.
It’s sound to me like you want one of the other methods.