Is it a good idea to backup different directories to the same repo?

Hi all! I'm a new user of Borg Backup, so don't know much. I tried to read the docs a little bit, but couldn't find a definitive answer.

Let's say I want to set up backups of \~/Pictures and \~/Documents. One way is to create a repo for Pictures and a repo for Documents. Another is to create a single repo and then create archives for Pictures with prefix "Pictures" and archive for Documents with prefix "Documents".

From what I read on the docs (and few experiments) it should work just fine, but I wonder if this is a good practice. I'm concerned that even if file contents will be deduplicated properly, will the list of files be deduplicated in the efficient way? May be there some other downsides on this approach?