First of all, in reported speech questions become statements, thus in your examples both 2nd sentences are wrong:
Reported speech: She asked me who the champion was / She asked me who was the champion.
Reported speech: She asked me what my favourite colour was / She asked me what was my favourite colour.
For the second, since when past simple converts into present perfect? In reported speech the main principle is to make one step back in tense while those 2 exist in the same spot on the timeline. One step back there will be past perfect, thus:
"She asked what the last film I had seen had been." Sounds abnormal, no one talks like that, in real life it would be something like: "She asked me about the last film I'd seen." or "She asked what last film I'd seen."