The USGS marker is located on a mound 300ft to the W-NW of the lookout tower. It looks lower than the base of the tower, but then why is the USGS marker there if it is not the actual highpoint? I wonder how many people miss that.
Your question raised my curiosity as well. Here are two possibilities. It may be the high point but, like you, I don't think so; we'll likely never know for sure. Alternatively, it may be roughly equal in elevation and if you saw the remains of some prior structure there next to it I'm guessing it was an antenna that was placed on the summit a while back to assist with other measurements. It may be that they chose a point that afforded better triangulation to other peaks as that's part of the purpose of those markers.
Most hikers assume the old lookout is the end of the hike. They are not looking for the actual natural high point on the peak to the west which has the benchmark.
The main description page is a bit vague on the trails to the peak. From the trailhead parking lot Trail 9 goes north, and is the shortest and most popular route. However, Trail 4 will also take one to the top, but it is a little bit longer than Trail 9. Trail 4 begins with a 1/2 mile segment leaving from the east side of the main trailhead parking lot that goes to the trailhead for Devils Tower alongside State Route 87. From that DT trailhead, Trail 4 then goes through a large, recently logged area (as of June 2011), which is not nearly as nice as Trail 9. The signage for both trails is good.
This peak is in Custer State Park. There is a $15/vehicle entrance fee that is good for 7 days in any South Dakota state park. Camping in the park is available but if you want to stay in park campground make reservations ahead of time. Cabin reservations require a minimum of 2 days advance notice.
We hiked up trail 9 and out trail 4. We went up the tower and then out to the benchmark. Our GPS recorded 7.98 miles and elevation gains of 1517 feet.
As previously noted, access is now $15 per car. Well worth it!
I am thinking that the markers that are to the W NW of the lookout tower are lower than the tower. One of the markers does say Harney Peak with an arrow pointing back to the SE, just S of the lookout tower. When you are at the entrance of the lookout tower and you look back to the S SE (where you came from) you will see some rock spears or spires. This I do believe is the top of Harney Peak. I didn't see anyway of climbing to the top of it. Hope this will help.
fee is now $20