I don't know the science involved, so I'm hoping someone else does. But is it more probable a giant creature of that size and capability would be more likely to exist if it were, say, a silicon-based lifeform? Or maybe arsenic? I'm not sure what element would make the most sense on the periodic table, or if it doesn't make a difference. I'm just trying to find a potential way around stuff like, say, kaiju would probably be crushed under their own weight, their lungs would collapse, their metabolism would be out of control, etc.
You are right that standard earthly lifeforms cannot grow to Kaiju size. In addition to your points, breathing and thermoregulation will be a problem.
Unfortunately, we do no know much about silicon-based lifeforms. They might face the same scale problems.
One workaround might be based on the world of Pacific Rim movie, where Kaiju are created by advanced alien race, and sent in to wreck our cities. These Kaiju can be biomechanical creatures: most of its large body produced industrially and powered by some sort of fuel. But this body is 'piloted' by a living brain, getting info from biological senses, and issuing commands via nerves. The mechanic body will run out of fuel eventually, but Kaiju will be destroyed by humans even faster.
Carbon is the best material you can use for larger life forms
The purpose of carbon in organic molecules is that it can form a maximum number of covalent bonds (4) which makes it an ideal scaffolding for making complex molecules. Without 4 covalent bonds making stable giant molecules like DNA would be impossible. The reason that Silicon & Arsenic are theorized to be possible acceptable substitutes for Carbon is that they also can form 4 covalent bonds.
That said, because Silicon & Arsenic are heavier atoms, and don't form any more bonds than Carbon, molecular structures made with these elements will as a general rule be more prone to fail under stress. In other words, if you have two large animals made of all of the exact same molecular structures where just the carbon is replaced, then the non-carbon ones will be heavier and more likely to collapse under their own weight.
No-selling large arms fire is problematic
A carbon-based lifeform being able to shrug off small arms fire like it's nothing is getting iffy. I'm under the impression small caliber pistol rounds won't do much more to an elephant than piss it off, for instance.
But kaiju are able to no sell large arms fire, like Hellfire missiles or artillery strikes. That is a much taller order. Blocks of solid metal are insufficiently strong to simply ignore a Hellfire missile like nothing happened.
So we are already in the realm of science fiction. The state of the art in materials science cannot tell us how to explosion-proof something (if it's even possible).