Propagation 'speed' of EM waves in air versus through conductive material
Not at all a stupid question. It looks like you’re reading a confusing paper. 

Electromagnetic waves don’t generally flow very far through conductors. Light reflects from metal, it doesn’t go through it. Radio doesn’t propagate in sea water. These things happen because the mobile charges in the conductor, well, move and that cancels the wave as it penetrates in. 

Glass and other non-conductors have charges that can move, but not freely. The motion of their changes acts to slow light down, but not completely cancel it. 

With no material, light moves at the speed of light in a vacuum because it is in a vacuum.