Here is my understanding - does this seem right?
4.2.1 Alternate:The Owner is 100% committed to having this in the Project. He would have to amend the contract to remove the alternate.
4.2.2 Alternate: The Owner is not certain if he will be able to have it in the Project. He would have to amend the contract to include the alternate.
Timing:
Alternate (or change) decided before bids come back: Addendum
Alternate known after bids come back but before signing: 4.2.1
Alternate known after signing: 4.2.2