They must default to using non twbt mode for spacefox. What you did was correct by moving it from the "fake folder" \raw\art and so on since I am pretty sure that isn't a df folder just one used to store those files but not activating them.
1. Would make so much more sense if they were named twbt_raw\art and so on since they can't work as raw\art anyways it would just confuse people. Heck it should be named if_you_want_twbt_move_these\art.
2. Idk what that rock click and save link is about he wrote it not me, I just quoted him. Anyways that folder seems to be a default in there anyways so that info was redundant. - Actually you have to copy over onLoad_gfx_Spacefox.init manually to either LNP\graphics\Spacefox\raw (it's in LNP\graphics\Spacefox). It's best to just copy and paste in the LNP\graphics folder, the tileset folder you want to change so you don't have to mess around to much and have an original in case you mess up. Wish they'd just add a twbt version this looks like a pain for noobs and experienced people if they want to use the twbt version since they will think they have everything already but don't. I know Dastactic is doing a let's play with spacefox but he does not have all of the twbt stuff included.
onLoad_gfx_Spacefox.init adds transparency, it could add other things but for now that's all it has.