The ceramic rod still takes material away, although not much at all, the final stage that some sharpeners use called a strop {its a leather strap}, does what you are talking about, just aligns the microscopic teeth, but that is only to be used after the blade is honed very fine...
How I used to use the ceramic rod was on a jig, 20 degree angle, equal on both sides, soft pressure, it is a good final step after a courser sharpening, final step would be the leather strop, I have a ken onion blade that I can get so sharp if I drop a hair on the blade it POPS it in half, that being said, if it touches my counter, cutting board, etc. it loses the edge very fast and its not fun to accidentally run down your nail..
I wouldn't worry about over honing, 6 passes on each side is all you should need, if you need more your first stage needs to be closer...
I used to be crazy about my knives until I used my first victorinox wavy edge, lol. I have some high end knives, I received a Dai Sensai knife as a gift from my employees one year {its a $1500 single knife, lol}, and I used to be crazy about how I kept their edges, sharpening, honing, stropping, angle jigs so I could get them perfect, I have a drawer in my kitchen with thousands of dollars in knives in it. But then the wavy edge taught me something, $40 will get you one of the best knives you will ever use in your kitchen!!!
Now I have an Ergo chef GF series on the counter {mostly because I like the looks and the steak knives are awesome}, and when cooking I use my victorinox knives that I bought from amazon, they come in a plastic sleeve no fancy wooden box with velvet liner, they have a plastic handle, white or black, no fancy full tang, triple pinned, teak wood handle, lol, just fibrox molded in black or white. But once you use that blade you will never mess with another knife. I always test a new knife with a soft tomato and some white bread, the wavy edge and victorinox slicer did as well or better than any shun in my drawer!!!
Anyway, I hope I answered your question and the extra info is free
if anyone is interested in the vics here are some links
http://www.amazon.com/Victorinox-Sw...id=1423050747&sr=8-7&keywords=victorinox+wavy
http://www.amazon.com/Victorinox-12...=1423050881&sr=8-6&keywords=victorinox+fibrox
or this one depending on what you use for slicing
http://www.amazon.com/Victorinox-Gr...1423050881&sr=8-14&keywords=victorinox+fibrox
them 2 will do about anything in your kitchen, but they have tons of other styles that can suit your needs...
http://www.amazon.com/Victorinox-4-...=1423050840&sr=8-2&keywords=victorinox+fibrox