The Tool Kit that comes with the KTM is the most comprehensive I have seen with a new bike. I think you could fix most things with it so I have left it stashed under the seat and added a small tubeless repair kit alongside it. The beauty of the seat design is that it is sealed up (so far at least) and the items stored under there don't get covered in mud and dust.
I added a Wolfman Peak Tail bag to the rear rack and it fits as though it was made for this bike. It is big enough to store a couple of Tubes, more tools and some wet weather gear. It can be expanded too if there is a need to carry more.
I removed the standard grab handles while I was going as I figured they would be easy to get your leg caught on while getting on and off the bike. To do so, I simply found a couple of bits of alloy and used them as spacers in place of the grab rail mounts.