This is 1 mio, I have a 5 mio version. Unfortunatly it is actually the limit on many fronts. While the D810 does have more resolution, I need to shoot in DX, where the whole insect is in frame. The 5 mio splat actually starts to show signs of noise, I don't have enough light to shoot with lower ISO, I'd need to recharge the batteries half way through and risk a drifting specimen. Also davinci on the free version and Postshot on the cheaper version have a limit of around 3k per image. Then.. postshot cannot reliably train beyond around 6 mio splats on my machine, I'd need a graphics card with more ram or train in slices. If (when!) I improve on all these fronts, a 100 mio splat or so will need LOD to run on any lower end hardware.
You are correct that focus stacking first leads to geometrically incorrect images, that is why I need to use as long a lens as possible. 90mm with 20mm extension on DX sensor is about as wide I can go, below that and the stacked images won't track anymore.
You are underestimating the problem of posing the unstacked photos. They are mostly blurry, only a thin slice is in focus, that doesn't track well. Also masking the area in focus is not trivial at all, years of research and programming voodoo went into stacking software, would be a shame not to use that.