But your question is still a good one to answer.

In general, if a "special" reservation code is used that has extra benefits, normally you will only get just those. It might be possible in certain instances though where a hotel could be convenced to switch/change a "benefit" for something else. In your example you mention receiving extra rewards points instead of a room upgrade. In most cases, you probably won't be able to get them to make that type of a switch. The reason is that for the hotel to give you more points, they actually would need to buy them at a cost where the room upgrade isn't really a direct cost to them (the room is already there and usable.)

So if you want to barter with a hotel on alternative benefits, you probably will have better luck if you are trying to switch from something that is a cost to them into something that they don't.