They are usefull in sword speedruns because they allow you to dash at them when close enough
^ Yes, this exactly. There are two reasons they are in a separate category. The first is that it is a pain to set up the skulls because you have to intentionally die in a specific spot. Setting up 3 takes a while and would make grinding IL times overly tedious. The second is that, because skull placement matters, people who do want to grind it out would need to approach runs differently than people who don't (different routes and strategies are opened up when skulls are allowed).
It's considered as a "skulled used" run according to the rules. It only matter if it's an Individual Level (IL) run since we don't make this distinction in the main level category. Did it happen during one of your IL run or do you just want to know ?
Il y avait un skull et je l'ai touché c'est une run IL level 11 je l ai soumise en skull used au-cas ou. There was a skull and I touched it, it's an IL level 1 run, I submitted it as a used skull just in case.