I did a "private group tour" with Top Komodo back in 2015 if you are on a private tour/excursion you had to make prior arrangements with the ship's Guest Relations Manager. Only passengers with a tour could go ashore. He wanted to see some proof of the excursion (email from tour operator will do), give us a meeting place/time, and escort our group to the tender, etc.
Top Komodos' tour included Komodo Island, a local village, lunch onboard, and a visit to a pink sand beach. Overall for the price (compared to HAL's excursion price) it was a great tour. At Komodo Island you walk in single file on a trail with a guide at the front and back. You stay on the trail; there was absolutely no wandering off on your own. We saw several Komodo dragons, most of the ones we saw were at an established water hole. Now the village that we visited (i.e. just walked through) was pretty filthy (both on land and in the water); and to visit we just tied onto a bunch of other boats at their dock. After touring the village we got back to the boat and they couldn't start the engine. Top Komodo had three boats there so they just tied ours onto one of the other ones to go to the pink sand beach. On the way over they served the "hot lunch" onboard, let's just say the lunch was OK but the cooking area on the boat wouldn't have passed any US Coast Guard "cleanliness inspections", etc. The pink sand beach was very clean which kind of surprised me as just across the bay the water was dirty in front of the village. They dropped us off back at Komodo Island to take a tender back to the ship. As I said before, it was a great tour; however, I know that was 9 years ago and things could have changed since then.