1. Preparing the upgrade kit

They did, It's called the MK4 assembly guide :) It seems like a pretty incredibly rare use case. It just doesn't seem like it would really be in the best interest of time for them to do that.
I'm not sure why the logic seems to be escaping you but if you have all the parts for the mk3s+ and all the parts for the MK 3.9 then all you need to do is follow the assembly guide for the MK4 and call it a day. It's a pretty simple solution. The only difference is the hot end and the x-axis, so when you get to those six pages you simply grab the parts from the upgrade kit instead of from the mk3s+Hope this helps the other one or two people on Earth that may have this scenario smiley face
 
 

Yeah, you have to think about the logistics side of it. Including tools in every box simplifies the process and ensures efficiency because they don’t make kits to order. The warehouse is set up to have these kits ready to roll. If they had to decide whether to include tools for each order, it would slow down logistics and delay shipping.
I suspect those tools cost only about three or four dollars. It's likely more cost-effective to give everyone tools than to pay for the extra labor and potential errors from forgetting tools when needed. If tools were accidentally left out, the company would then have to package and ship them separately, causing delays and incurring additional shipping and packaging costs.
And honestly, who complains about getting extra stuff for free? You can donate the tools, give them to your kid to play with, or recycle them.