Thank you very much for your detailed response.
Product Customisation does look like the best solution for sure, however based on the roadmap, I feel it probably won't be ready in time.
Product Options may work as you outlined and although it might be cumbersome to administer, I'll give it a try first.
I have used Cart Properties on another project, and you are correct, it would only work for a one entire order, so the user would be limited to one package of cupcakes only per order.
Your last solution I am still thinking about, I understand the idea, just unsure of how multiple packages would be added to the cart if needed (which I am sure will be the case).
I really appreciate your thoughts and will update this post with either a working solution or more questions and issues, if encountered!