We have seperate management and although SOPs are much more harmonised there are some differences in philosophy.
The EAT not starting the APU on the 757 is a carry over from the A300, though why they started doing it on that I'm not sure, when Air Contractors had the A300 they certainly never had the policy of not starting the APU. (At least if they did have the policy it was dropped on saftey grounds very quickly)
As for the cycles run on the APU on the 757 I would think they are automatically recorded by the QAR rather that just on an assumed 2 starts per sector.