Was the SNES's graphics processor programmable?

Grall is correct, SNES/SFC's vid chip can only scale/rotate the background layer without the help of additional chips.

the scaling/rotating bosses and objects you see in most games are backgrounds made to look like sprites. (and you only see one of them.. not a bunch of independently scaling/rotating objects)

games that do have scaling/rotating sprites have additional chips.
 
If you observe how a ship moves away in the distance in FZero, you will notice that instead of transitioning smoothly to a smaller looking object, it dramatically shrinks to a smaller and eventually smaller size. However, in the GBA version, the scaling is done smoothly, with no noticeable transition points.
 
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