From what I can tell, they are only giving credits (with later retrofit) on options that are standard to a trim level. For example, on LS trim, front and rear parking sensors are standard equipment so there's a $50 credit with later retrofit. On LT trim, heated steering wheel is standard and has a $25 credit with later retrofit. I'm sure there's others, but those are the two trim levels I've been studying the most. The note about retrofit is included on the window sticker.
If the feature is optional equipment and there's limited availability, then the option is added to the constraint list and up to allocations. They won't build the vehicle if it's not given an allocation for that option.
Either you wait until your dealer gets an allocation for all of those options, or you start changing your order so it can go through and not be held up by constraints.