Interesting idea, I would be a bit concerned about training customers and not confusing them.
How about something along these lines?
In Hikashop I would define a custom ITEM field called Shipping Package with a select box and values like:
- Default shipping
- Package 1
- Package 2
- Package 3
- Package 4
Customer could order 3 bottles using Package 1 option and then one bottle using Package 2 option.
The shipping plugin would then calculate the shipping price (or maybe give customer more choices) depending on the products and selected custom item field options.
Depending on complexity may need some custom PRODUCT fields to control what features are available (and associated shipping prices) for different products.