What’s the fission cross section for U-233? IOW, will it burn up in the core along with the thorium?
If the fuel is removed before the optimum time for Thorium consumption, there is more U-233 present. It is possible to operate the reactor to optimize U-233 production, which produces a lot more U-233 than otherwise.
Whether you "burn" U-235, U-233 from Thorium-232, or Plutonium-239 from U-238, there are always fission fragments -- highly radioactive light elements produced by the fission process. These are always nasty. I don't know all the details of the Thorium cycle, but anyone who tells you that there is no radioactive waste is lying, just like they are lying about no bombs.