Core: Cleanup: Replace direct calling of dunder methods on objects

[Mysteryem]

What is this fixing or adding?

Calling the dunder method has to:

1. Look up the dunder method for that object/class
2. Bind a new method instance to the object instance (if the method was defined on the class)
3. Call the method with its arguments
4. Run the appropriate operation on the object

Whereas running the appropriate operation on the object from the start skips straight to step 4.

Region.Register.__getitem__ is called a lot without #4583. In that case, generation of 10 template Blasphemous yamls with
--skip_output --seed 1 and progression balancing disabled went from 19.0s to 18.8s (1.3% reduction in generation duration).

From profiling with timeit

        def __getitem__(self, index: int) -> Location:
            return self._list[index]

appears to be about twice as fast as the old code:

        def __getitem__(self, index: int) -> Location:
            return self._list.__getitem__(index)

Besides this, there is not expected to be any noticeable difference in performance, and there is not expected to be any difference in semantics with these changes.

How was this tested?

Ran generations before and after

[silasary]

Code looks good and change is reasonable