The rules state that the scrambler, egg, falling mass, and cushion must fit in a 100.0 cm x 50.0 cm base and a 100.0 cm height. Does this imaginary box include the energy propulsion system? If not, what are the parameters for the energy propulsion...

Per rule 3.a., the "Scrambler" has 2 components, the egg transport (vehicle) AND an energy propulsion system. Both parts of the "scrambler" must fit within the prescribed dimensions.