You can set the scale of the y-axis in stackedplot using the undocumented NodeChildren property. However, the vertical reference line and text that tracks the mouse position will no longer work and a warning will continually appear when the listener is invoked. Therefore, that warning should be turned off (see below).
h = stackedplot(1:50,[exp(1:50)',exp(1:.5:25.5)']);
ax = findobj(h.NodeChildren, 'Type','Axes');
To set the yscale of a specific axis, n