Is it possible to use the same reference shot for every time the camera starts or does it always start with making a reference shot and optimise from there?
I'm not really sure what you mean.
The first exposure is based on whatever the Canon firmware would have used, either auto or manual. I think CHDK menu overrides should work too, but not sure it has been tested.
For every subsequent shot, it analyzes the raw data of the preceding shot and calculates a target exposure that would result in the scene being "perfectly" exposed as defined by the script options.
The target exposure calculation is essentially deterministic, i.e. target = f(scene), independent of Canon settings or anything that happened before. However, the shot-to-shot change is limited to keep the results smooth. This based on the change in the preceding exposures and how large a change is needed to achieve the target.
The result of this is that the script takes some time to "settle" from the initial, Canon firmware calculated shot to the script calculation. For Canon auto exposure under normal lighting, the change usually isn't big. If you start at night, or used manual settings, it could be quite large.
Because the exposure is calculated based on the previous shot, the script works best for fast intervals and/or scenes that don't change too rapidly.
It would be possible to make the script use a throw-away initial shot to meter the scene, but I'm loath to add more options unless someone has a real use for them.