In إِنَّ زَيْدًا أَبُوهُ قَائِمٌ, the *whole clause* occupies the nominative syntactic position of khabar. Its individual words are parsed separately.
In إِنَّ زَيْدًا يَقْرَأُ, the verb’s own indicative/nominative mood is distinct from the syntactic status of the whole clause as khabar.