Answer
Presence and separation are two different experiences.
When you see someone in person, all your senses are engaged. It is a complete, multi-sensory experience. But when you simply remember someone, that experience is incomplete. Remembrance is a form of separation.
As remembrance deepens, the desire to have the Lord's direct, personal presence also increases.
Consider a simple example. A student is studying away from home. The parents speak to the child every week over the phone, yet they repeatedly ask, "When are you coming home?" Communication is continuing, but it does not satisfy them because they long for the child's physical presence. That longing is separation.
Similarly, Śrī Caitanya Mahāprabhu taught the mood of separation. Although the Lord is present everywhere, His most intimate and beautiful form—Śyāmasundara—is eternally engaged in transcendental pastimes in the spiritual world. The devotee longs for that direct association.
Even though the Lord is present in our hearts as Paramātmā, we can still experience separation from Him. Spiritual life involves repeated cycles of separation and reunion, with progressively deeper realizations of the Lord.
One first realizes Brahman, then Paramātmā, and finally Bhagavān.
As Vaiṣṇavas, our aspiration is not to develop separation from Paramātmā in order to behold Him directly. Our goal is to attain the personal association of Śrī Śyāmasundara in the spiritual world.
We understand that the Lord's Paramātmā feature performs a different function. He oversees the material creation, resides in everyone's heart, and guides all living beings. Therefore, we certainly have a relationship with Paramātmā. He is our Chaitya-guru, the supreme controller who sanctions the results of our actions.
When we perform devotional service, we depend upon Him for the results and leave those results to His will.
Yogīs may aspire to directly perceive Paramātmā, but that is not the path of the Vaiṣṇavas. Our aspiration is to act in such a way that Paramātmā becomes pleased with us, blesses us, and grants us the spiritual intelligence to distinguish spirit from matter.
Paramātmā helps us discriminate between matter and spirit, but it is the spiritual master who teaches us how to develop devotion (bhāva) for Kṛṣṇa. By observing the devotion of the spiritual master, we learn how to become devoted ourselves, and through him our devotion ultimately reaches Śrī Kṛṣṇa.