John, you are absolutely right about the tags. That is sort of a big deal I don't want to downplay that issue.
However, I personally believe that .wav is the only way to go for ultra high-end systems simply because it removes all doubt that the format is compromising the sound in some unknown manner, however slight. The fidelity of the source material is important enough to me that I am unwilling to accept even the slightest chance that something is being lost for some reason we don't understand. It is simply one variable removed from an equation that already has too many variables.
The problem is one of confidence. With .wav and error correction you can be reasonably certain that you have taken your archive of redbook CD as far as it can go. So when the time comes to audition that next upgrade or tweak, you can be confident your source is as close to reference as possible.
That said, am I confident I could distinguish .wav files from apple files in a blind test? No absolutely not. Apple lossless sounds very good to me. But again, do we even know what we should be listening for? Do the difference, if there are any, manifest themselves on all recordings, at all volume levels, or on all equipment? Will a more advanced system five years from reveal some distinction that my system today wasn't capable of? I don't know, and I don't have to know because I .wav.
Use compression only if storage space is really at a premium.