You tell me that An alpha particle is just a helium nucleus without any electrons -- two protons and two neutrons. But well ruther Ford was experimenting the gold foil experiment that time neutron was not discovered so how they get that Alpha particle is made up of 2 protons and 2 neutrons

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.