Before I had a universal player, I already owned three DVD-Audios: The Blue Man Group's Audio and The Complex, and The Polyphonic Spree's Together We're Heavy. I owned them because I saw on their packaging that I could play the DTS layer. And man oh man did it sound sweet!
But the universal player was purchased because I knew I would someday be dabbling in SACDs as well, so now I could listen to both the DTS layers on my DVD-Audio discs, as well as the hi-res DVD-A layer. Flipping between the two, I think I prefer the DVD-A layer. The sound is not a huge step upward, just a baby step or two. It's a bit richer, the sound stage just a bit more defined, the instruments just a little bit clearer.
So for me, I prefer the "Multi Ch Input" over the digital (in my case, DTS/dolby digital 5.1). But it's not the hugest of differences.
However . . . I can say that I prefer the DTS layer over the dolby digital 5.1 layer on the Blue Man Group's Audio disc. The sound is far more dynamic and richer. Without a doubt.
But that's just me. And bear in mind it might be my equipment's fault, which is probably low-end to most of the people in here . . .
cheers,
supervij