The original psychonauts cost 13 million, it only makes sense for the sequel to cost more. Also, I think there is some miscommunication or Notch is making stuff up because I don't think it was ever going to be just "a couple of million".
That said I don't really blame him for not going good on a twitter semi-joke, and I'm sure the price has gone up from the original estimates.
And I don't think you can really blame Double Fine for facing reality and upping the cost of development. Psychonauts 2 would be a much bigger project than reds, which is already going over it's ~3mil budget.