The transparency has no effect because there's nothing behind it. You're stacking the bars end-to-end, not on top of each other.
y1 = 1:10;
y2 = fliplr(y1);
% two bar plots, one atop the other
hbh(1) = barh(y1); hold on
hbh(2) = barh(y2);
cm = ['b'; 'r'];
for k = 1:numel(hbh)
hbh(k).FaceColor = cm(k,:);
hbh(k).EdgeColor = 'k';
hbh(k).FaceAlpha = 0.2;
end
legend('Graph 1', 'Graph 2', 'Location','best')
