The Gold Cup is a CONCACAF tournament (Analogous to the African Nations Cup or Euro 20xx or Copa America). The Confed Cup is comprised of the winners of each of the 6 Confederations' Cups plus the World Cup champ (Italy) and the host nation (RSA). The only team that is playing in both is the USA.
Let's say Canada won, they'd be in the same position as the USA because they'd be attending the Confed Cup + the Gold Cup. Any CONCAF team would be really hindered in the tournament they don't choose to take their A team.
Having two tournaments at the same time would only work if they were say Euro and African Nations. There's no conflict between the two.
Agreed. The tournament should really move from every two years to every four years, either opposite the Confed Cup so as not to interfere with WC qualifying or opposite the WC (i.e. at the same time as Euro 20xx).