Nice to know the kit functions properly in regards to the cam chain adjustment, now to correct the issue with the nut.
I don't want to file flats, because there will no longer be any zinc coating on that part and it will rust. The only way I would do that is if I can get some sort of plastic or rubber end cap like a tire stem cap to cover the end in an attempt to avoid rust. There other possibilities though.
I looked at the pictures, but am not totally sure if I am seeing things as I think I am. I may have a solution I use on the KLX250. I use an allen nut from a Yamaha SR500 exhaust - IF there is any clearance for it. It is 13mm in diameter, I am not sure I see that much clearance there in the pictures so you will have to let me know. I can turn the nut down tight against the end of the bolt and with a dab of blue LocTite on the thread it should stay put. I can also use a shorter bolt since it appears you cut about 10mm off the 110mm bolt. Let me know if there is 13mm of clearance there, otherwise it is plan B.
If that can't fly, I will look at using an M6-1.00 adjuster bolt with the same jam nut/acorn nut set up since that should clear. The pressure on the bolt is linear, in compression, and in line with the center axis of the bolt so the smaller size will work fine. It will just look small. Not a big deal. Shoot, I think that's the size of the thread on the Tokyo Mods tensioner is even smaller, possibly an M5.
We will see if the allen nut can work first. You can see it below by the exhaust on the KLX. We went to that because they couldn't access the adjuster that easily when a large diameter aftermarket exhaust is used.
Hopefully there is enough room for the allen nut to turn without hitting the casting. I use the jam nut on the KLX because I prefer to lock the nut against the allen nut, which would not damage the threads at all and the jam nut cost is only about a nickle.
Get back with me and I can mail out the allen nut if it will work. Otherwise I will get bodies with the smaller thread made for me.