Guest Relations, in general, can handle anything that the Will Call windows can, as well as the ticket windows. However, I know of at least one case where someone was explicitly directed to the Will Call window from GR.
Even though the GR lines may be shorter, I'd expect the per-guest time to be longer as they are probably dealing more with issues than typical transactions.
Of course, at the MK the Will Call window is the GR window most of the time. Anyone there this week noticed if they are using the other building due to the crowds?