Does a Dropbox permission set control which files a user can see?
No. A permission set controls what a user can do in Salesforce, whether the Dropbox File Manager loads for them and which admin functions they can reach. It has no effect on which files or folders they can see. Dropbox decides that.
The File Manager always connects with the individual user's own Dropbox account. Each user sees exactly what their Dropbox account can see, based on who owns a folder and who it has been shared with. This applies to administrators too. A user with Dropbox Admin can manage workspaces and see every folder mapping record in the org, and still be unable to open a particular record's folder, because that folder lives in a colleague's Dropbox and has not been shared with them.
When a user hits a folder they cannot see, the File Manager shows a Request Access button. This sends the folder's owner a Salesforce notification and an email asking them to share the folder from Dropbox with the requesting user's Dropbox email address.
Note: If you want consistent file access across a team, manage it in Dropbox rather than in Salesforce, ideally by using a Dropbox Business Team Folder as your workspace, so everyone on the team sees the same folders automatically.

