Who can be an applicant or partner in case if the organisation is registered outside the eligible area of the Programme, but it has a unit operating in the eligible territory of the Programme, which is not registered?

According to Guidelines for Grant Applicants 2.1.1.1. (including Footnotes)
In order to be eligible for a grant, applicants and partners must be located (be registered or have a registered operating office) in the eligible area of the Programme, meaning that:
•  Organisation’s statutes or equivalent documents according to the national legislation should demonstrate that the organisation has been established by an instrument governed by the national law of the country participating in the Programme. In this respect, any legal entity whose statutes or equivalent documents according to the national legislation have been established in another country cannot be considered an eligible local organisation, even if the statutes or equivalent documents according to the national legislation are registered locally or a “Memorandum of Understanding” has been concluded. This obligation does not apply to international organisations.
and
•  Eligibility of organisations or their registered operating offices must be proven by providing a registration certificate or an equivalent document according to the national legislation indicating that they are registered or operating in the eligible area. Exception to the requirement of registration applies only for International Organisations.