1. Will this work same for custom schema's?
Yes, it will work in the same way here
2. Do we need to add Organization Unit field in all custom schema?
See the other existing reply
3. After adding Organization Unit field in all custom schema, do we need to link it back with OOTB organisation unit schema with one-to-many relation?
No, this is not required. Activating the option mentioned will automatically add this link and all things required.