nope. The size in meters of a particle has nothing to do with how many electrons/protons get ionized, that only has to do with the charge of the particle that flies through matter, to first order. And yes, it is definitely not every atom that gets ionised, the probabilities are really small.

But charge is much easier to measure than displacement. That is exactly why we don't use the size. It is much much MUCH more likely that an atom is ionised some way than that a particle actually hits (and then displaces significantly) a proton, neutron in an atom.

I did find an error though, those 10000s of ionisations (which depend heavily on material that the particle flies though) should be per mm, not cm. But that is a factor 10, not millions

(ps: don't mix SI and imperial units)