At that time they did not know the composition of the alpha particle, they just knew the mass and charge of it. In fact, they didn't even know that the alpha particle is also just a nucleus because the nucleus was discovered by that experiment only.
Only after a certain number of years, the scientists understood the relation between the charge and mass of species and the mass and atomic number, and to make the students learn quickly they teach in that way.
Hope you understand by this.