Complex sentence: There are no standard NYSDOT reference markers on any of the highways; instead, the Thruway Authority posts their own mileposts, which (aside from the mainline) bear special Thruway codes.
Split into simpler sentences: There are no standard NYSDOT reference markers on any of the highways. While some of the Thruway system may have unsigned NYSDOT reference numbers, the mileposts of all of the highways (aside from the mainline) bear special Thruway codes.