Could be not wanting to have part of the sugar sucked up into the group, 3-way, etc. Wouldn't be a problem if backflushing is done often anyway.
One thing I don't like when I do them (using raw sugar anyway) is the coarseness of the sugar causing a less dense puck/faster extraction. Standard white sugar doesn't seem to cause this due to being much finer, but doesn't have the same flavor either. I might experiment with different layering technique(s) with the raw sugar or grind a bit finer when doing them. Either way should offset the problem.
Probably the craziest thing I've done similar to this was using honey instead of sugar just to see the effect. Was messy to say the least and not at all what I expected. Much easier to just add that to the cup. Never know till you try something. Best part of it was that it wasn't my machine :)
For the same reason we don't do flavored cappuccinos, etc., and the same reason we always suggest people taste their drink before adding anything. Because the coffee tastes flippin awesome on its own, so why ruin the experience right out of the gate.