The only thing that I do not use iTunes for is importing CDs, since the iTunes encoder is not bit accurate. I use xAct for the rip, encode to apple lossless and then transfer to iTunes.
I recognize the iTunes Apple Lossless encoder is not bit perfect. I take it xAct's encoder is bit perfect? Can you speak to what type of compression savings you're getting with xAct's AL versus just keeping Wav's?
The apple lossless encoder in iTunes works perfectly if you are encoding a file (i.e. wav or aif, I have done multiple phase tests to check this out), the issue that I have with iTunes is the actual ripping of CDs to any format. For the sake of speed, Itunes does not do an error check against the original CD image after it has imported a disc. When you import a CD with xAct, it takes longer than iTunes, but the software repeatedly checks the files that it is creating against the physical disk image to check for and correct errors, resulting in a bit accurate import.
Regardless of the apple lossless encoder working well inside iTunes, I still use a separate encoder program for creating my apple lossless files. It's a free program called XLD and I use it for the following reasons:
1. You can convert flac to apple lossless directly, without decoding to wav or aif first.
2. There is a simple drag and drop menu
3. When you import/convert a file with iTunes it automatically adds those files to your default iTunes music folder, which can only live on one hard drive. The iTunes system of importing/converting is not very practical if you are spanning data over multiple drives. By doing all of my converting outside of iTunes, I can drag and drop any files and folders I want into the iTunes screen and they will be indexed but not moved from the drive where I want them to live.
To keep iTunes from always copying files to the iTunes music folder when you drag them into iTunes, make sure that you have the "Copy files to iTunes media folder" box unchecked in your advanced settings. Once you have this box unchecked, iTunes simply acts as a playback index for what ever media you drag and drop in there.
The compression for apple lossless is pretty much the same as flac.