Lossless is lossless but in realtime, things IMHO aren't quite so simple.
I used to rip to Apple Lossless, storing them on my iPhone. I remember going to a store demo a few years back armed with a CD and the iPhone 3GS.
I put the 3GS on a Wadia iTransport feeding the Ayon CD5S vs the CD playing on the CD5S and I was surprised how much better the CD sounded. The iPhone sounded lifeless and lacked "energy". I was not expecting that. My friend at the same demo asked me if I ripped to WAV. I said no. He told me to try that.
So I converted a playlist of my favourite and familiar tracks to AIFF (I figured AIFF was just WAV with meta data) and went back the following week to do the same comparison again. This time, the difference was less apparent.
Based on that experience, I converted my entire library back to AIFF and deleted the Apple Lossless and have not looked back. I also rip new CDs into AIFFs directly.
So in theory, Apple Lossless is lossless - that's how I managed to convert my ALAC library to AIFF overnight. But the playback chain is something that we are only just coming to grips with.
That's why even though USB (synchronous) can be bit perfect, an asynchronous USB interface can sound better still. That's why different software players (JPlay, Audirvana, BitPerfect, Amarra, PureMusic) can sound different. Heck sometimes even different versions of the same player can sound different.
As for WAV and AIFF, my understanding is that WAV sounds better again. The difference is that one is big endian and one is small endian but for some reason that can cause a difference in playback.
I use AIFF primarily because I can keep meta data inside the file. WAV apparently can support it but the support for that enhanced format is less well established.