Sanitizing sanitizes all the surfaces the sanitizer touches. What it cannot do is get under dirt and slime and whatever else might still be in the bottle. Bacteria will hide there, and come out into the beer if it's not removed.
So what you do is first clean to remove the dirt and stuck on stuff, then sanitize to kill anything on the surface.
That's sanitizing. You could also sterilize the bottles--boiling water would do that if it's held at that temp long enough--which will kill everything, even bacteria under a layer of soil. Sometimes people will sterilize bottles in an oven, leaving them at some temp above 212f for a specified amount of time.
My own method--others do something similar--is to triple-rinse a bottle when I'm done with it. I don't fill them all the way, just a couple ounces or two, swish around, then pour out. Three times. I then inspect to see if there's any apparent residue.
Then the bottles are inverted in the dishwaster upper rack and sent through a normal cycle. The bottles in mine end up clean. But they're not sanitized, so just before bottling I rinse them with a vinator; dip the mouth of the bottle in the solution, then a couple squirts, let drain, and fill w/ beer.
A vinator is one of the better buys I've made. Speeds things up, keep the bottle caps in the reservoir where they're sanitized, and everybody's happy.
