Yes, iTunes also uses the same Core Audio framework. In fact, even iTunes on Windows uses the same code base through the Quicktime-for-Windows libraries it runs off of.

I prefer to encode with afconvert on the command line because it gives me a few more options for tweaking things, that I don't have access to in iTunes (or "Music" as it's called these days). Additionally, I use a simple shell script that handles all of it when for example ripping a whole CD.