Change to allow "staging" geometries to be run on existing hits

To allow checks of reduced scenarios for staged ITk insertion, we would like to be able to re-run on existing HITS with geometries that have fewer Pixel modules. This implements a few checks to avoid access/processing of DetectorElements that don't exist in these reduced geometries. These are false by default, which should maintain current behaviour.

FYI @tstreble @ncalace