Those lines create flat upper and lower surfaces. The upper and lower surfaces otherwise would appear conical.
The easiest way to see that is simply to ‘comment them out’:
figure(5)
[x,y,z] = cylinder([0,1,1,0],100);
% z([1,2],:)=0;
% z([3,4],:)=1;
mesh(x,y,z)
Then restore them to get the desired figure.
