You'll hear the difference when MDS kicks on with the exhaust valves open. Sounds like absolute ass. The vibration your feeling is likely due to the way MDS works. It closes off the exhaust valve and lifters, creating a small air gap that the piston uses to "bounce" just like it would after detonation, so while not producing power in the cylinder the pistons and cams can continue their rotation.
Reminds me that blacksmiths always hit the hammer on the anvil to keep their rhythm going, it's the same in the MDS system. I assume the extra vibration we feel is due to this.
I can confirm on my 24' while in 4cyl mode that I get vibrations under load, while still staying in 4cyl. What you're experiencing is normal MDS Hemi. The only thing I can think of is if there was a lifter failure and it's now making contact with the cams. The vibration could be from them hitting and overtime creating a flat spot on the cams which would cause irregulararities in detonation.