There is a lot of speculation about the pizza which, now we know for a fact she didnt eat it, has to be put aside. There is nothing to say the pizza made it back to the flat. There is nothing to say the girl cooked it, started cooking it or was interrupted cooking it. Or to assume someone else ate it there and then disposed of the packaging for some reason. Or took it with them afterwards to eat it at home.
The pizza - which the police allowed the public to think had possibly been eaten by the victim, so locating the victim back at her flat - was not eaten by Ms Yeates. It has nothing to say about her being in the flat.
If anything, the fact she didnt eat it would suggest more that neither she nor it made it back to the flat.
I always thought that the killer took the pizza almost as an afterthought. He was hungry,and it looked good. An individual without any conscience at all about killing might well do that, IMO.