1) If you take away Uranium from a thorium reactor you will rather quickly lose criticality, so you won't be making any new protactinium. Thorium breeders run very close to steady state, and only make a very small fraction of fuel more then they need.
2) I'm pretty sure there is a rare reaction that you will get protactinium-232, which has a much shorter half life the protactinium-233 (about a day instead of about a month) but it can't be chemically separated. It will decay to U-232.
The nature article is alarmist, and not practical. It would only make sense if you had a separate neutron source that was not a thorium breeder, and probably will still have a good amount of U-232. Since you have a neutron source (probably a light water reactor) why you wouldn't use the extremely well understood methods to make plutonium from U-238 is beyond me. You quite literally just need to put uranium metal in the neutron flux for 1 month and chemically separate out the plutonium. Much easier, if I was designing a nuclear weapons program I sure as hell wouldn't pick Thorium.
2) I'm pretty sure there is a rare reaction that you will get protactinium-232, which has a much shorter half life the protactinium-233 (about a day instead of about a month) but it can't be chemically separated. It will decay to U-232.
The nature article is alarmist, and not practical. It would only make sense if you had a separate neutron source that was not a thorium breeder, and probably will still have a good amount of U-232. Since you have a neutron source (probably a light water reactor) why you wouldn't use the extremely well understood methods to make plutonium from U-238 is beyond me. You quite literally just need to put uranium metal in the neutron flux for 1 month and chemically separate out the plutonium. Much easier, if I was designing a nuclear weapons program I sure as hell wouldn't pick Thorium.