If memory serves, and it is likely that it does not in this case, the abominable "Extinction" did involve some aspect of the Xindi hunt. I think it is mentioned only at the beginning of the episode. Someone correct me if I'm wrong here.To me, Similitude and Twilight (along with North Star, Doctor's Orders, and Extinction (ugh!)) are sufficiently understood as stories all by themselves to be considered standalone, even though they may have subtle repercussions that show up later on in the arc.
I think all of the episodes are self contained during season 3, and understandable without knowing the entire Xindi story. To me, this is not what makes an episode a standalone.
Agree that Sim is not a standalone and that Doctor's Orders is a standalone.