But I've seen this metaphor in action and I've seen the damage it does....................
If you want your organisation to run like a well-oiled machine, then its elements should behave predictably - but its elements are people and people have a chaotic, emotional, unpredictable aspect to them, which is the antithesis of machine behaviour. So trying to build a deterministic organisation out of unpredictable pieces is not going to have a happy outcome.
And then there is the environment in which the machine operates, comprising social, political and economic elements, all of which are intrinsically chaotic.
So, just at a theoretical level, trying to create a machine-like organisation out of unpredictable bits in a unpredictable world really won't cut the mustard.
And, surprise, surprise - it doesn't work in practice either!