The Ballon D'or has always had a heavy weighting towards International and Continental Cup competition. Henry was beaten to it by players who won the CL. Owen and C.Ronaldo won it after winning the Uefa Cup and CL.
I suspect the reason why it has has such a heavy weighting, aside from them being more coveted than domestic titles, is because voters don't actually watch and follow all of the best players across Europe. While, everyone is always tuned in to major CL and International games.
I'm not a Liverpool fan, but I've watched them against Leverkusen, Milan, PSG, City and Madrid outside of facing us. I sure as hell wasn't watching when they played the other 17 PL teams, so I think domestic form just doesn't carry as much weighting when deciding who deserves it.