There are three issues I see with putting a rack(s) into an S&S case.
1) I have the 10 inch case and it is a tight fit for just the bike. I have thought about trying to put the rack(s) in there but I don't think I could. Either was I have to take another case for my other gear and I just put the racks in there.
2) When the bike is packed there is a lot of potential for metal on metal contact. Putting metal racks in the box will increase this by quite a bit and probably cause even more scrapes and chips.
3) My bike in the case gets close to the 50 pound airline limit. I don't want to get too close to it so I use the other case for everything except the bike.
My bike has 700cc wheels and I think it is bigger than yours. I don't know the exact height but I am about 5'11", if that helps.
I created
step-by-step photos of my bike packing process so that I could repeat it without having to "discover" the best way every time. I take it with me when I travel with the bike. I suggest you do the same thing as it will save you "figuring it out" time whenever you have to pack or unpack the bike.
I do pack the fenders and the tires in the case. I have to remove both to get the bike in the box. I also have to remove the front brakes.
By the way, get cable splitters for the cables that go across the couplers. They will save untold amounts of time by not requiring cable reconnection when pack or unpack the bike.