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See, we can use shortcode (and there can actually be many other ways) to display a product with checkboxes. The problem is not with the display. It is when the 'Add to cart' button gets pressed - the core code of CouchCart accepts only a single cart item at a time.
When you are submitting a product with, say 3 checkboxes checked, you are actually adding three items to the cart (on your website too, although you show it as one line the cart, the number of items added is 3).
We can possibly add a routine in the middle that intercepts the submit with multi-checkboxes and converts it into single lines but that would involve custom coding (i.e. cannot be done natively with existing functionality).