The EMP comes from the detonation of the nuke outside of a medium (atmosphere, water, earth, etc)... Or rather all Nukes produce an EMP, just ones detonated within a medium do not produce the mass of free electrons.

From what I understand, the pulse is a two part phenomenon- the first part is the bulk plasma produced by the energy release displacing the geodynamic field, and the second part is when the debris of the weapon slam inot the ionosphere producing ionization.

In general, especially the first 'pulse' (plasma displacing the deodynamic field) is an effect of interaction with the Magnetic Field, but there is nothing 'designed' about it, aside from just detonating the weapon outside a medium to insure a plasma is formed in the magnetic field. There is nothing unique to the plasma, all weapons produce one on detonation, and the only difference is size of yield and efficiency at producing gammas.

Let me put it this way. A Semi truck does not have to be specially designed to shred a Geo Metro. All that needs to happen is to arrange a circumstance in which a Geo Metro is placed in front of a Semi at speed. Its just a question of use and context, not of design

If you have some sort of link to infomation that is contrary, I'd live to see it.