It is since younger brothers of father mostly married into matrilineal castes like Kshatriya-Nairs and Ambalavasis, and they did not have any heir to perform Pitra Karma for them becuase children in these unions belonged to mother's family and they performed Pitr Karma to their
maternal uncles or karnavars instead of their fathers. Hence, the eldest son in a Namboothiri Brahmin household performed Pitr Karma to his paternal uncles along with his father.
The younger brother in a Namboothiri family was allowed to marry within community (i.e. Namboothiri women) only if the eldest brother did not have any son to pass in the paternal lineage.
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