To obtain the desired effect (always show the patches in-dependably on how small they are, put the 'EdgeColor' the same color as the 'FaceColor'.
p1=patch([10 10 500 500],[0 axisLim axisLim 0],[1 1 1 1],...
p2=patch([9000 9000 9010 9010],[0 axisLim axisLim 0],[1 1 1 1],...
I think this behavior should make sense with another pair value variable, such as ('appearIfThickerThan',Units), where units could be specified with percentage axes units or inches or so on. The 'FaceColor',and 'EdgeColor' should work the same way if I use 'EdgeColor','none' or 'EdgeColor' with the same color as the 'FaceColor'.