Alright, I get the picture a bit more clearly now, I think. In the sake of completeness is your listening evaluation, I might suggest sticking with your clean WAV files you're generating from EAC, and then converting those same files to Apple Lossless on the PC using
dBpoweramp Music Converter with the
m4a, mp4, m4b & aac codec installed. Using this codec will require that you additionally have the free
Nero Digital Audio+ codec installed.
If you then use iTunes to play back the WAVs and Apple Lossless files, just make sure to visit Edit > Preferences > Playback and ensure that no effects are applied on playback (in iTunes for Mac, Sound Enhancer is enabled by default, whereas in iTunes for Windows, it's not). Also, disable Sound Check if it's enabled.
In order to make this listening test fair, I think it important to use the source WAV files to generate your other files for comparative listening rather than using the Mac to create new test files. For years, there have been claims from many users that audio extracted from audio CDs on Macs sounds quieter than audio extracted from audio CDs under Windows, and this even when Sound Check is not enabled on the Mac. I can't fairly comment on this, since I rip my audio CDs to lossless files exclusively on my PC and then move the files to my Mac for other purposes.