As far as ESI is concerned they are covered by ESI Act and contribution should be paid at the place of their working, ie, in India. for EPF also the same rule applies but I doubt if they come under international workers and if so their contribution will not be limited to 12% of Rs 6500 but the entire PF qualifying amount (Basic+ DA mainly) paid in India will attract PF. But I am not sure whether persons of Nepal origin migrated to India for permanent settlement in India is a foreigner whose details are required to be given to the nearest Police station etc. If they are free to do job in India, they will have same status like any other PF member.
Regards,
Madhu.T.K