If you are using MongoDB Atlas, you can control access based on field values using Realm Rules. This would allow you to use one collection per entity while restricting access to the client that the data belongs to. So you could have a rule that a user can only see data that matches the company associated to that user.
If you are not using Atlas you can control access on a database or collection level. So you could use that to restrict access for a database per client for your scenario.