Realistically I don't think there's any reason you couldn't just make a switch that turns MDS on and off. I think the big reason it's so highly controlled on the factory PCM is because they want it to be seamless. Doesn't seem like you could hurt too much by turning cylinders on and off whenever unless you catch something right in the middle of some operation like a valve possibly closing early when the lifters bleed down on activation. Not that this would necessarily hurt anything, but it could make the engine run noticeably odd for the brief period when it transitions.
I heard the rumor in the past that MDS works better on the auto cars because the torque converter can soak up a bit of the "bump" in the engine when it transitions modes. I can tell when my parents' 2012 Ram is in 4 cylinder mode most of the time because there's a slight vibration and you can feel it smooth out when it kicks all 8 back in. I'm guessing a stick would be a far more noticeable "thud" that may make the average driver worried.