Linear power supply vs SMPS (losses in transformer)
If you want a truly optimized converter and/or compare different topologies directly, this is one way how it is done: 

In an overall system optimization, you are taking into account losses of all relevant components, especially power semiconductors and inductors and transformers. You start with a topology, then calculate losses, size and cost estimate (BOM) of the whole converter for a given parameter set (e.g. switching frequency, transformer core material, power semiconductor...). You loop through a large number of parameter sets, sort out designs which don't fit the specs, and look for the best compromise in e.g. cost vs. efficiency ("Pareto optimization"). 

It is complex and time-consuming. Getting the right models is not trivial, and one has to find a compromise between model accurracy and model complexity. You would have to employ a circuit simulator and an inductor/transformer design tool. 

Here is one typical converter optimization example: Google Little Box Challenge, see Fig. 10 for the general procedure and Fig. 12 for typical results. 

If you want to compare different topologies (referring to your question), you have to run the system optimization procedure for the different topologies, with different semiconductors, different transformer core materials, and so on, and compare the best solutions directly.