Interesting. This actually has distilled down to a very good question, and to be honest, I haven't thought about it from that angle before. Is this the question:
"What is the difference in propagation equations for an EM wave in free space, versus one confined to a transmission line? And why does there appear to be a fundamental difference in the equation for the propagation velocity for these two cases?"
This is basically what I am confused about. The reason I start to question this is because in one of the problem from a book ask to find the propagation velocity of EM wave through sea water where from calculation it is consider good conductor and the velocity turn out the be in 10EE7 range which is an order slower than light. And If using copper \sigma = 5.8EE7, the velocity will be even lower. But in stripline case, velocity is simply about speed of light divided by square root of relative permeativity. On top of it all, EM wave don't even penetrate metal very much at all and guided wave in stripline travel as far as the dielectric allowed.
I'll have to think about that some before I can try to give a useful answer. My intuition says that the difference lies in the directivity of the transmission line (TL) case -- that is, the EM wave that propagates along a TL is directed down the TL by the conductors of the TL (coaxial, or twisted pair, or stripline, etc.), so the loss is dominated by the skin effect resistive loss on the conductors, and the parasitic conductance loss in the dielectric of the TL. The only "loss" in a free-space EM wave propagation (not in a conductive media like seawater obviously) is the growing surface area of the wavefront, which gives you a power loss over distance with a 1/r^2 coefficient.
I'll PM a couple other PF'ers to try to get them to address your question, assuming I'm interpreting it correctly. BTW, since this is in the homework/coursework area of the PF, we can't do your work for you (per the PF Rules link at the top of the page).
I am not in school, I am a self studier. Actually I had been an EE for close to 30 years and manager of EE for 14 years. I am just studying as a hobby! I have six or seven books on EM, I am not saying I read everyone in detail, I did read at least two in very detail and go through the others. I don't recall anyone compare the difference.
You have asked a very fundamental and interesting question, though, and have shown a lot of your own work. Can you take what I've said about the constrained nature of the Poynting vector and different attenuation mechanisms for a TL versus free space, and see if that can explain the equation differences that you are encountering?