The Admech often operates on BlackBox tech; they have no idea how it works, they just assemble it. Plus, they use bio-computing, so there are little chunks of animal brain tissue in a lot of computers.
I always sort of figured that they were like Apeture, sticking simple AIs into things that don't really need them, like the Turret's Empathy Generator (and attatched to it, a small Empathy Supressor).
Basically, Machine Spirits don't "calculate" the way a normal program does; it's a hard-wired bundle of instincts that thinks the way an animal does. They "feel." They're very good at their particular task, but have to be babied and placated sometimes, and can also be persuaded. They're also incapable of...self-adding, or whatever it is that happens when super-AI start making themselves smarter.
Plus, people make machines. And the arrangement of physical objects can invoke/influence the warp. If all those little molecular machines in a living cell can make a ripple in the Warp, then nothing stops a gun from doing so as well. Plus, people project beleifs onto their creations, so you get lots of effects like Jaheed's old rifle Judy. or Dust, from His Dark Materials.
So, this combo of animalistic psudo-AI, ignorance about tech, inefficient manufacturing, and the wonkyness of The Warp and human belief means that the common "machine spirit" belief is pretty consistent with how imperial tech functions.