In most (but not all) cases, it is just substituting what would be a discount (in this case $2) with a lump of points. Sometimes, there is a bit of both. Either way, it is probably the manufacturer paying for it.
I've had cases where the bonus points value exceeds the cost of the item....
That's a clear profit or what I call an "arb"
I' fund one of these once in a blue moon but most of the times its a too small value to retire off
As for these bonus points. I try and keep in perspective the bonus points. Eg buying a more expensive brand of cat food for the bonus points even though my cat wouldn't know the difference.
I try and keep things in perspective in my points hunting quest and not pay more for a smaller return