The Paramatma feature of God is the overseer of the material world in sristi lila. He presides over the cosmos, each universe, and each atom. Thus he is described in three phases. The point here is that he is all pervasive (Visnu). There is no place where he is not.
The description of his being in the heart the size of a thumb, etc. is for conceptualization during meditation. His omniscience is not dependent upon his being in the heart, although he does appear there when his devotees meditate upon him. This is explained by Baladeva Vidyabhusana in his Govinda Bhasya (1.2.7, 1.3.24-25.)
God is all pervasive and all knowing. He manifests in relation to the material world as the Paramatma and in the spiritual world as Bhagavan. Because the Paramatma is a partial manifestation of Bhagavan, the omniscience of Paramatma must also be present in Bhagavan.
In Vaikuntha, Narayana’s omniscience is tied to his love for his devotees rather than being employed for the purpose of witnessing the deeds of the jivas, as in the case of the Paramatma. Narayana is all knowing in the context of a loving relationship with his devotees.
In Goloka, Maha Vaikuntha, the abode of Krsna, God’s loving relationship with his devotees shifts from formal, as in Vaikuntha, to intimate. In loving intimacy, God’s omniscience necessarily recedes to the background to facilitate that intimacy. For example, in Dvaraka Krsna sometimes asks Uddhava for advice as if he were not omniscient in order to experience an intimate loving exchange with him, subordinating himself to his devotee.
In Dvaraka his omniscience is prominent and his divine ignorance less so. This is reversed in Vrindavana, where his omniscience is clearly subordinate to his divine ignorance, in which he thinks of himself as the son of Yasoda, the friend of Madhumangala, the lover of Radha, etc. rather than God. While God never losses his omniscience, it becomes less important to the extent that love permeates the relationship between himself and the individual soul.