What's the difference between Cuemix and Direct Hardware Playthrough?

There's no difference. Under MAS with the PCI-324 card, Direct Hardware Playthrough is essentially Cuemix. Enabling "Auto Cuemix Update" simply gives you the ability to control Cuemix levels within DP or AudioDesk's mixing board. The Master Fader level, however, should still be controlled within the Cuemix console.