Is cortical magnification in the visual system related to synaptic pruning, or is it a separate developmental or learning process?
No, it's not due to synaptic pruning. If it were due to synaptic pruning babies would have better vision(esp. Peripheral) but that is not the case. Babies only have better hearing. 

No, it is not exactly a learning process. Most of the foveal developmental starts during the prenatal period and complete by 18 months postnatal.Most of the inter-individual variance have been linked to genetic factors. There is no conclusive evidence for environmental factors affecting the foveal development. But there is speculation for possible environmental factors. 

Reference : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658155/