OK, so that's a pretty clear majority in favor of merging "Special within story arc" and "Special outside of story arc". The fact that I wasn't able to come up with any super clear examples off the top of my head should have been a give-away :-) Still listening to additional feedback coming in, but I'll lean towards that then.
In that case, both of them would be displayed in the episode list together with the normal episodes in that season. Would it make most sense to sort them all by airdate, or to still keep the specials at the top/bottom of the season's list?
Also, both of them will be shown in the watch list - I don't think this should even be a preference. (Insignificant specials would either always be hidden, or be hidden by default with a preference to add them in)