The Pre-amp section is designed differently.

It's firmware can be updated.

It has two XLR output modes for recording both in standby(studio) mode and direct mode which uses the tube power section and therefore cannot be used in standby mode.

To me it sounds much better and reacts more to your subtle nuances of picking style rolling off the volume vibrato ..etc etc.. you can feel that tube vibe better whereas the Mark I needed some mods to get closer to that "tube" effect.

Then as you siad there's all the bells and whistles in the fx dept. which are very nice.