I would actually argue that the editing is pretty straightforward, and systematic even. A very general understanding of after effects is all you need, as I hope I can show better when I can make the workflow video..

..but in a nutshell, there are two components: the live action and stopmotion clips (obviously). The hand is recorded first, so that if the stopmotion needs to interact with the hand I can frame by frame overlay the video of the hand over the current stopmotion view (to make sure the positioning is setup correctly).

Then in after effects, it's a simple matter of using masking or the rotoscope tool to "cutout" one element or the other; though it varies, I usually will cut out the stopmotion character (sometimes a simple ellipse around the figure also works for most of the frames until the two or three frames where the hand touches the figure). The cool thing is this is almost as plausibly done using blender (open source) and its tracking/compositing workflow, which means ultimately anyone can do this without fancy software (though it tends to help).  The last steps are to make sure the colors match perfectly (even with the exact same settings, differences arise between video and photography) and then applying some (timewarp) motion blur (the minifigure looks odd if it has no motion blur while the hand does, so that's a big part of bringing it all together)

Moo-ack Productions! Latest release: "Design Flaw"~Patrick W. Crawford