Bob,
The ROVs that Cameron uses have no arms, no ability to interact with the wreck. They carry a camera and lights and are designed only to record. The Mirs carry manipulator arms, but will be restricted from interacting with the wreck in the manner that you suggest. Because of the new protection treaty, NOAA is enforcing a strict no-touch policy for everyone other than the salvor-in-possession, RMST. Where the actual wreck is concerned, even RMST must observe more exacting restrictions. In order to do as you suggest regarding the "mystery box," an argument must be made about the historical necessity of determining its function, and that argument will have to gain approval from NOAA and RMST, at the very minimum. Cameron does not have the resources to pursue this process for his next expedition.
The area of the well deck that you described was well covered by NOAA in 2004. No skylight is visible in that area, but there is also an accumulation of sediment and debris between the cranes and the B-deck bulwark that make it impossible to say for certain whether or not a flush-mounted skylight might be found there. Again, Cameron's ROVs would be unable to clear the sediment build-up to reveal the actual deck underneath, and the area is too hazardous for Mirs to approach closely.
The water tank that you mentioned was imaged extensively in 2004. All piping, valves and connections are visible and well lit. Again, when the NOAA images are released to the public, you will want to look for these images.
There is no rectangular feature over the W.C. where you have indicated in the collection of images on your website. The 2004 images look closely at this area and whatever showed in the earlier ANGUS imagery is either long gone or was a misleading clue. Without having the image to show you, you'll just have to take my word for it for now. I am confident that the NOAA images, when released, will bear me out.
Cameron has specific goals in mind for his next expedition, most focusing on the interior. In order to gain permission for his interior exploration, he must satisfy NOAA that he will not damage the wreck or otherwise treat it with disrespect. Of course, a lot of eyes will be following his ROVs, looking for detail that might chance to pass by the cameras' lenses. Some mysteries, however, will remain mysteries because they lie just outside the camera's range or underneath a layer of silt.
So, if you're primarily concerned with exterior details, I recommend that you study the NOAA image archive (I counted over 6200 images and 87 video clips during my analysis effort) when it is released for public access. Cameron's focus is on the interior, but there are plans to include some exterior locations, such as the well deck (and don't expect much emphasis to be given to the foredeck and stem...those have been well covered in the past).
Parks