Those lines you see, I think indicate hidden surfaces.
Do this test to see the difference:
Create a cylinder with a capped end. Select the cap surface and extrude it.
(Uncheck the parameter: *Remove Original* )
Align normals, make it double sided ... you should see the hidden surface at the join.
Repeat above but CHECK the parameter: *Remove Original*. The hidden surface is removed as you do the extrude ... no line at the join.
Also note if you join two cylinders at their capped ends then the *Optimise Surfaces* will only remove ONE of the two caps.
Hope that helps.
griff