Would Nigma be able to use A MAN REBORN to prevent this 3rd action damage?

No. Edward Nigma's A Man Reborn? allows you to put an action token on him instead of the character being given the non-free action. The Colossal Size ability causes unavoidable damage on its own...not as a result of any token.

Question about Dr. Manhattan's action rule set. Here it is

How does this apply to the new colossal rule?

From the way I read it, it says it can be given a non-free action, so Dr. Manhattan doesn't necessarily have to be given the third non-free action, and instead be pushed when he has two action tokens and not take pushing damage. Is this correct?

The intention is that characters like him with that type of rule will not be affected by the change to Colossal Size.

Intentions aside, the way the new rules are worded, they just granted all colossal characters the Masters of Evil TA. If this is the case, then a colossal would take unavoidable damage when taking a non-free action when it already has 2 action tokens.

It is interesting to note that this ability is not specified that it is non-optional, and it has not been specified that it overwrites the old rules. It does bother me that as it stands it does say

When this character has two action tokens, it can be given a non-free action. After the action resolves, deal it 1 unavoidable damage and do not remove action tokens from it at the end of the turn.

emphasis on the when. This would imply that unavoidable is dealt regardless of what other abilities said colossal might have, since they all say they avoid pushing damage, and now it is unavoidable damage instead.

This just makes me wonder how more convoluted they fix is going to be to make it that older colossals do not take this unavoidable damage.

Abilities in this game default to optional. All they have to do to make the ability optional in the next PAC is neglect to put (NON-OPTIONAL) in front of it.

That is not going to happen.

If Colossal Size was suddenly optional, you'd have Galactus ducking down behind a Moloid every time someone tried to draw LOF to him.

You could make just the new portion optional. Some feats have done it.

Groot just got even radder.