I think you're getting a bit confused with the terminology. The Magni is a headphone amp, not a DAC. It takes line-level analog audio input and amplifies it to drive your headphones. A DAC converts a digital signal to a line-level analog signal. The logitech dongle is both a dac and a headphone amp (if it's what I'm imagining).

If your question is "will it make any audible difference if I use a dedicated external DAC instead of my motherboard's line out".... maybe? Audio DACs are a mature technology and a competent "low end" implementation is transparent for the purposes of human hearing... so it depends on the quality of your motherboard's audio output and how much of a golden-eared audiophile you are.