All of the markers in the book were physically located, photographed (the marker and a context photo), geolocated, etc. The book has the identifiers, locator verbiage (summarized and converted into text an ordinary person can use to find the marker), and the latitude/longitude, along with an assessment of how easy it is to find it, whether it's accessible to someone in a wheelchair, and if it's "family friendly" (easy to access for someone with small children). The website has the photos and any other notes created since the book was published, along with links to their NGS and Geocaching.com pages if they exist. There's also a general history of the various surveys that were done in the park to explain why there are so many, why they were monumented, etc.
There are several that I found that are not listed in the book or the website. I made the decision to not include those that were somewhat unsafe to get to, such as those along the side of the road where there's no pullout nearby (and thus, no place to park your car), those in thermal areas where no boardwalk was available, those in areas that spend a good deal of time closed for bear or other wildlife management functions, and so forth. The NPS expressed appreciation for that.
Of those 550, a good number of them probably no longer exist. There are 53 that I was unable to locate, most often because the road has been realigned since they were monumented and in all likelihood have since been destroyed. There are also many in the backcountry that I didn't have the opportunity to hike to.
All of the marks I found are listed (subject to what I explained above). This includes about two dozen that are not listed in the NGS database, mostly NPS benchmarks placed in the 1970s as a part of their re-engineering of the water system. There are benchmarks from USGS (including the CVO), BPR/PRA/FHWA, USCGS/NGS, USDI/NPS, and even one from the old General Land Office (now the BLM).
I don't know the answer to that question. If you contact me via private message, I'll give you a POC in USGS that might be able to address that question, though.