I can relate to some of the concerns that the OP brings up.
What I would like to see on e-junkie that I think would help tremendously is the ability to define not only how many products fit in each container, but also how many containers fit inside each other.
I know that it can be done - right now there is only options for small med and large "tubes". However, if you have more than just 3 standardized shipping containers, I think you can see how this can only be mildy effective.
For example I would like to specify that 3 small envelopes can fit into 1 large envelope. 2 large envelopes can fit into a small box. 4 small boxes can fit into 1 large box and so on.
I know that with shipping calculation you do your best estimate to arrive at a determined shipping price, but I think that being able to organize your containers would be a very powerful tool for many sellers.