Personally I think the people who are on the amnesty better start to make some plans as flights out are getting fewer and more expensive. The immigration bureau have lost a lot of income, they won't want to be losing anymore.
I am not sure on the processes, I believe that there will be a screening point at the ferry terminal, hopefully someone will be able to clarify once they have got here.
yes but the OP stated that he will more than likely be in Bangkok which means he maybe somewhere else. Now if he is somewhere else it would more than likely be quicker to use a smaller provincial immigration than the trek and wait at CW, which is why i made my suggestion.