The difference for me is that the marker restrictions can be worked around through clever drafting. Heck, if you're only bringing one JL Marker design, Champion isn't more rewarded than any other of their choice classes. Batman III, Zatanna I, Constantine, and Green Arrow I works as a "Justice League build" even though there's only one Champion.
Black Canary just having a Champion callout is a harder line that pushes more towards Champion-only JL army building. It's just a slight D20 boost, hardly a big deal, but it does feel like a misstep to me to take the faction in that direction (direct Champion synergies), especially when we already have the Superman Family stuff doing that.
