In your example of using bottles to contain a liquid being transported.
All containers have a certain amount of required and excess material to enable them to hold a desired quantity of liquid. In the case of the bottles this material is in the thickness of the bottle, both the walls and the base. The large the container the thicker the walls and the base. Also, bottles have a funnel arrangement at their top (the opening) through which the bottle is filled and emptied.
Two half litre bottles will have two such funnels and will require extra material that a one litre bottle, which would the same capacity as two half litre bottles combined.
As an indication of the work/energy required to transport anything, a convenient unit of measure is weight multiplied by distance carried. For heavy haulage items this is tonne-kilometres, but it could also be kilogram-metres.
If 6 tonnes of stuff are being transported 10 km then the effort required is 60 t-km.
In your example, you would need to know the total weight of the filled bottles: bottles + oil + caps + labels and multiple that by the distance being transported for each situation and then compare the t-km for each scenario.