I have done the simulation (diameter sweep of the pillar) for both cases with metal and without the metal layer, as you suggested to renormalize the transmission to divided the transmission value/ Purcell factor; as Purcell factor = Dipole power(f)/Source power(f). So I did the normalization for both cases (even without the metal transmission being less than 1). So I am getting plots like this.
Hope this plot is clear. T(transmission), PF(Purcell factor), Renormalized_T(T/PF). Red and black lines are normalized T without metal and with the pillar.
And plot for T and renormalized T behaving quite differently. My main goal is to go with a diameter that will give the maximum transmission.
Here I wanted to compare the situation with metal and without metal, so I compared by doing renormalization in both cases. Is it right to do renormalization even if I do get transmission less than 1?
Another thing is there are many peaks are forming in transmission, are these corresponding to different modes? Like the first one is fundamental mode and so on?
(In this simulation I took fdtd region xspan, yspan and zspan 2, 2 and 3 um respectively, and stretched coordinate PML, steep angle with 40 layers.)