It's ok to pack the ATS box together with the generator sets in next order, I'll do what you request and help you avoid spend more money on customs, you know the officers are always the bad bad guys.
For the container unloading, firstly thanks for your effort on this, you must have done a very good job. To be honest, I was very surprised to hear this "problem" from you, we two companies have been working together for 3-years, your company used to buy even bigger genset/pump from me, this is the first time to hear this "problem" from you or any other customer. It's easy for me to do what you request, but I think your solution is not a good idea to solve this problem, what if our future order machines are evan bigger? How you plan to take the machines out? You see that this container is quite full, if we didn't load the container as planned, it's possible that there'll be goods left hehind. Attached pls find the photo that my factory loading container, pls find a good way to solve this problem, this should not be any problem as your company is a very big and good one, keep in touch with this in future orders.
My another suggestion, when you book the container from your forwarder, pls do ask your forwarder about the shipping schedule, pick up the container asap when the ship arrived your port, this will help you save time and money on customs clearance, I know your port only provide free container stock for 1-week, right?