Considering the nature of the two mods, I started out by asking the folks over at Muluna (here, if you're interested in the specific bug report: https://github.com/nicholasgower/planet-muluna/issues/292)

Unfortunately while he did see what was going wrong, I will quote his response:

"The best solution for mods that create new versions of assembler 3 is to scale the data fluidboxes by the same ratio that they scale the fluid fluidboxes. That would be the best solution. Either that, or only copy the first two fluidboxes in the assembler. I believe this issue is fixable, but it's best done by Kryzeth."

If you could point me to the right lines to edit I'd be happy to do it myself, this is just a bit beyond my ability to do unguided. I suppose I could dummy out the assembler 3, but that is like 99% of my reason for downloading mini/micro machines to begin with.

Failed to load mods: Error while loading entity prototype "mini-assembler-3" (assembling-machine): PipeConnectionDefinition: position must be inside of entity bounding box. position={1.000, 0.000}, leftTop={-0.598, -0.598}, rightBottom={0.598, 0.598}

No need, I already figured out the issue and have a fix ready. I was waiting to release it because when I tried applying the same fix to its sister mod, Micro Machines, the data pipes wouldn't connect properly after rotating the machine or re-selecting the recipe.

I believe this is related to the collision data of the new pipes being infinitely smaller than the collision data of standard pipes (which connect properly to micro machines in the same situations), but increasing the collision so that they connect makes them no longer walkable, which I imagine was the purpose of reducing the collision data to begin with. It's also possible that there's a bug exclusive to micro machines that is preventing the data pipe connection, I can't be certain.

Of course, the micro machine issue technically has no bearing on the mini machine update (since that one worked just fine with the minor fix), so I guess I'll just release this one and live with the mismatched compatibility (and minor version numbers) for the time being. Fixed in v9.2.7

And if you're just genuinely curious on the inner workings of this mod, the data pipe related fixes were added around lines 33-48 in func.lua, within the function Data:fixPipeConnections() (the pipe changes aren't actually done programmatically, since the pipes need to be in exact positions, and it's not a simple matter of scaling down the numbers, since the pipe is off-center on a 2x2 entity, compared to a 3x3 entity, the new pipe positions all have to be added manually)

Outstanding, and thanks for the detailed response.