Well, yes; we could choose an appropriate 'level' to discuss this at but I still say the idea of modulation does not relate just to EM waves. It is a strictly mathematical issue and it seems quite reasonable to expect Modulation to be something that could be associated with any form of 'Wave'.
Physics is, as you say, a subset of Maths and there are many possible Unphysics answers. Actually, 'a particle' never behaves like a wave. You need a lot of them for the two explanations (particle, wave) of a phenomenon to converge.
I guess people use the "like Radio Waves" description as a shorthand for 'waves and all the associated theory'. Also, Modulation is usually analysed in terms of Frequency.
You could, for instance, velocity modulate a beam of electrons and that would be modulating the de Broglie wavelength of the electrons. But there is no actual frequency (afaik) associated with these electrons, unless it's f=v/λ?. Likewise, if you were to alter the local fields inside an atom, (Zeeman and Stark effect??) you would be changing the 'wavelengths' of the electrons in it, which would be a form of modulation. But, again, what is the 'frequency' involved? Perhaps that's where the flaw lies - with 'mathematical', mechanical and EM waves, there is a basic c = fλ involved. Is there an equivalent for the the waves associated with matter?