Regarding the topic of the special rooms being visible from the start...
Ages ago, for use on the normal HQ board, I've cut out pieces of black cardboard in the shapes of all the rooms. My intention was to have all the rooms (except entry) covered by black cardboard from the start of the game, and then removing the cardboard pieces as each room is explored. The idea was to make it even more visual which rooms had been explored and which had not, to enhance the visual experience of discovering the interior of an area that had until then been "kept in the dark". I haven't had the chance to playtest it. (The idea of keeping also unexplored
tunnels visually "in the dark" with cardboard does not seem practical, I think... so doing it with only the rooms might be a good compromise.)
Back to the Sjeng's Dark Company board special rooms... with the above mentioned black-cardboard idea, revealing the special rooms too early would not be an issue