Very good point about the differences in the lossless formats like AIFF, FLAC, and Apple Lossless. That is their point: to save exactly what is in the music. Apple Lossless and FLAC need to expanded by thier music player before you hear the music. I have a 2005 iBook that runs FLAC into my HiFi system with no problems. FLAC will not play in iTunes. Vox and Decibel will play FLAC files directly. Vox is free and in the App Store. Decibel is about $35 and in the App store. Both applications will change the sample rate to match the music.
On the iPad try FLAC Player. It is about $10 and it will play high Def FLAC music and change the sample rate if you are playing on external DAC through the camera connection kit and a powered USB hub. There is another, free version that has a similar name and icon. I wasn't happy with it.
There are other music players in the iPad/Pod/Phone App Store but they may use the iPad internal audio and that will down sample to 41.1 or 48 KHz. You can't tell truly unless your DAC shows the sampe rate of the incoming music.