The Airport Express is surely more "hi-fi" because, as you say, there's less processing (only downsampling to 44.1 kHZ due to Airplay's limit).
The wired MacPro/mini way is even more "audiophile" (actually it's perfect from an audio point of view). I've a Mac mini connected to a DAC through USB. Using iTunes with an app like
BitPerfect you even don't have to switch manually the sample rate in Audio MIDI Setup in order to match the sample rate of the songs. Everything is done automatically and the Remote app let you remotely control the playback as you pointed out.
BitPerfect unfortunately crashes from time to time. It's related to the last versions of iTunes. Previous versions of iTunes worked fine. Developers are struggling to figure out a solution. There are other hi-res-iTunes companion apps available, though.
I, like many other "picky audio guys", understand what are you trying to accomplish. Managing your audio library natively with iTunes and enjoying hi-res audio at the same time.
I like Apple in many ways: I wish they would be more audio friendly in this sense. AppleTV should simply have an option to enable bitperfect playback. At least it'd act like an Airport Express. I know, 48 kHZ is the standard in the video field – still, it sounds to me a silly decision to force upsampling.
I own an AppleTV 4 which doesn't have the TOSLINK output. I have to use an audio HDMI-TOSLINK de-embedder to hook it to my DAC. Just another example of Apple complicating audio users' lives.