You're making the fundamental mistake that all notes that are written down are the same. A midi-file isn't a score, it's a recording of the playback of notes. A performer can sit down at a midi enabled Steinway Grand and record their performance into a midi file, then they can play back that exact performance on the same piano and it will sound identical to the original. If you were to listen to such a playback with your back turned, you would be unable to tell if the pianist was playing, or if the midi was.

Programming a machine to play something back in just the way the composer wanted is the same as performance. The composer get to become the performance artist interpreting and setting their own will, their "soul" as you want to call it, into the machine. So that their music is interpreted and heard exactly as they wished it to be. It's no different than if the composer were to perform their own compositions.

You may not like the instrument being used here, or the way in which the composer has expressed their intent in the recording, but it's exactly as they intended.