Out of curiosity, I put out an inquiry to a representative with the OCSJ. They do indeed have the coordinates of the markers, but were hesitant to share them because of accuracy problems (I suppose they were previously provided to the public at some point, as Guy mentioned, and then people complained). Also, the coordinates have not been kept up to date with the latest changes to the trail route.
OCSJ crew will always have the best info. The long-awaited state map is supposed to be coming out very soon and the state seems to really really mean it this time (as opposed to when it was supposed to be coming out soon for the past many years now and they apparently didn't really mean it).
What I've heard is that what's coming 'real soon now' is a new printed Batona Trail brochure, plus new display panels (those big 3'x4' signs in metal frames at various points along the trail which have a map and other info). I do not think they are doing anything new with the existing on-line map (spstrailtracker.nj.gov or the NJ GIN data set), which may already represent the most up-to-date data they have.