"Both the Denon and Yamaha have very low jitter and harmonic distortion/noise floor. So why would they be expected to sound different? "
Because they use different DACs? Because they use different power supplies? Because they're designed differently and use different parts?
You can't base how a component sounds off of a piece of paper that states how a component measures. It doesn't work that way.
I've used both of these CD players and prefer the Yamaha in my particular system. (I upgraded to a CDS-2100 from the CDS-1000, though the sound and presentation is similar between the two). YMMV. If you go through a dealer that carries both, you can always exchange the unit if you're unhappy.
I will say this, Yamahas in general take forever to break in and settle down.
The Denon didn't take nearly as long to acclimate.
The Denon's controls, response and load time is superior to the Yamaha (which can be rather clunky to load and use).
Again, both are fine players, so it's up to you to decide which route to go.