For # 1:
Couldn't you add a button to 'Add another box' in the Restrictions and Dimensions section?
Then if a Product had multiple boxes in it, you would have them on the product page and calculate shipping from that. It would be MUCH easier than having hidden options without a 'No' selection. By having the hidden options, I now cannot use the options on other products because the 'No' has been removed in the code.
For example, we sell golf simulator packages. So using our ProX Plus as an example. This product comes with 2 boxes. 1 contains the golf simulator and accessories. The other box contains a Stance Mat. Rather than creating separate products with $0.00 and having to use the options method (without a 'No' option), I could simply put the dimensions in for each of these boxes.
For # 2:
Yes, I saw the option for 'Group Package' but this is a global setting and not an individual product. Thus, if I turn that off it will cause every item to ship separately correct? So, if someone order 3 bags of golf tees it will want to charge them for 3 boxes where these can easily fit in 1 box (along with many other accessories). This is why I believe that having an option to 'Ship product separately' would be better. Then, if you have a sealed item that nothing else can go in the box - it doesn't allow other items in. Meanwhile, you can still have a box for small items that do not have to ship separately.
For example, we sell golf simulator systems. Items such as Stance Mats, our projector pack, computers, etc. all ship with nothing else in those boxes. Meanwhile, things like golf tees, club tape, foam golf balls, etc. can all be combined into any size box needed. So if someone purchases a computer, club tape and foam balls - we would ship this in 2 boxes. The computer (which would be labeled as 'ships separately' and a second box with all the accessory (tape and foam balls).
Hopefully these examples clarify and you can understand the importance of these features so they can be added in the near future. I'm sure we are not the only customer that ships in this manner.