Well, I always do a secondary and I also bottle. Now, secondary is a total misnomer since there isn't really a secondary fermentation. When you rack the beer into the clearing tank (which is really what it should be called), the goal of this carboy is to condition and clear up the beer. You can also dry hop during this time. Fermentation should be finished before you rack into a second tank, because you remove it from the yeast cake. Still, you'd be surprised at the amount of crud that falls out of the beer and is left on the bottom! The pro breweries call it the "bright tank".
Then, after 2-3 weeks, without disturbing the sediment on the bottom, I put my priming solution into my bottling bucket and rack the beer quietly into it, swirling with the tip under the surface of the liquid, so it mixes well without aerating. Then I use the bottling wand and bottle.
I guess you could prime in the secondary, and then bottle from the secondary with a siphon, but there are a couple of issues that come to mind. One is that it would be hard to mix up your priming solution well, since you'd be pouring it into the carboy and you don't want to stir and mix up the sediment or aerate your beer. Second, it would be much harder to control the siphon compared to the bottling bucket/wand.
I've made countless batches of beer this way, and aeration has never been an issue.