On the contrary, imagining the electron as a smeared cloud (a complex-valued wave function with a bunch of specific properties), is pretty much the only way to explain chemical bonds.
The confusion stems from semantics. Sure, nobody claims that an electron has been detected at two spots simultaneously, not because it does not happen, rather because to say that you need the premise that the electron is a point particle with a position.
Sure, it is useful to claim that the electron is a point particle - in plenty of circumstances it does look like one. But modern physics pretty conclusively has demonstrated that it is actually something described by a wave function, that is most certainly smeared over space.
I am a physicist, so I will leave the discussion of whether "smeared" is a good word for it to the philosophers and linguists. It is a good enough word for me, when I try to derive properties of atoms.
Sure, but the crucial points is, quantum fields are just mathematical tools, the universe is filled with particles, not with quantum fields stretching across all of spacetime. The fact that it is under some circumstances convenient to mathematically treat a large collection of particles as a quantum field does not make that quantum field a real thing, just as describing the traffic flow on roads with fluid dynamics as a mathematical modeling tool does not mean there actually exists a car field spanning across all the roads.
[...] yet others are happy to just shut up and use the model to do calculation that just work.
This certainly seems to works in many circumstances, but I think it is not really good enough to treat the point raised in this thread. When you are discussing whether an atom is mostly empty space, you have to be more careful. Just because your mathematical model uses objects that fill the entire atom does not necessarily mean that this is true for the actual atom, it could just be an artifact of your mathematical model.
However, please also accept that for many people (me included) the model of quantum fields is much more real, and the model of point particles is the one that is just a mathematical illusion.
We invented quantum fields to make locality obvious but this is not possible without making the description redundant and so we just declared that one physical state corresponds to an entire equivalence class of mathematical states.
So I really don't think this is a matter of philosophy, they are not equivalent models.
The wave function may be smeared out over space, but that does not mean that there is an electron everywhere. Electrons are never at two places, never has anyone looked and found the same electron at two different places at the same time.
What happens if nobody looks is up for debate, whether you think the electron has no position, whether you think it is guided along its path by a pilot wave, whether you think it split into zillions of copies in different universes, or whatever.
But the electron or many electrons filling out its entire orbit is not compatible with any of that or any experimental evidence. At least as far as I know, I am not a physicist.