I think that's related to a similar issue I have in my own save where my category amounts don't add up to my resource amounts. It's a deep bug that is going to take untold hours to find - maybe next patch.... aaaaand I spoke too soon.
Even on a save that didn't do the "Claim All" thing, HQ after the cheats finished running is reporting as having a good few thousand more resources than it should - I suspect the ones that would've been used for the tutorial-mandatory plots. I think this might be something that'd only affect people who cheated straight through past the Tutorial part?
Also... it appears that doing the topmost "HQ Disasters" setting to OFF in MCM doesn't actually blanket disable them all - I'm still getting Fires. The individual toggles do work, though. this was the one thing I hadn't checked until now
Will check into the disasters thing.