Electronic devices create steam bubbles if powered and suddenly submerged, plasma-based systems more so, especially transporters, cloaking devices, conduits, etc. The list goes on and on. Steam bubbles. Where they existed the hull is another question.
What scale are you using for your BoP? Are you taking your cues from the matte painting, which is probably not a good idea. Or, as you taking it as comparable in size to the Grissom? (which would be around 100-130 m)
I have wondered this myself especially since I needed to know for a story. In reviewing ST:III there is a circular dome with a light underneath the BoP, visible when the ship first decloaks above the merchantman trader ship and as it enters orbit around Genesis, before destroying the Grissom. I then took a look at ST:IV. First of all, its very apparent that Sulu is bringing each piece of the tank seperately. As Scotty is guiding a piece in from the top and sees Gillian down on the ground, you can see the thick packing crate the factory built around the plexiglass. From the inside, you can see McCoy observing, and for whatever reason, a packing crate in place instead of the plexiglass being removed. Once Gillian is beamed aboard, you then see the same packing crate that Scott guided in with the bottom removed and the plexiglass itself being lowered into place. That proves each panel for the tank was brought in seperately. Also, that there is at least an opening on the top of the ship. Once they crash land in the bay, you can see Kirk pull the explosive release on the bay doors and then swim down to get out of the bay. He then swims up to the surface. I believe the bay doors are the dome on the bottom of the ship, also visible in this movie when they first depart Vulcan and again as the BoP hovers over the whaling ship.
When Gillian (and we) look up, Scotty is visable from the waist up, the upper part of his body is above the clocking 'field', the lower part inside the field. Could Scotty, because he was so close see inside the field. Could Scotty see his own feet, the birds hull amd the opening he was guiding the crate in to . Or was he doing it all by 'feel'. T'Girl
The ship is scaled according to 109 meters overall length (stated by the designer). The whales are scaled as adult humpbacks, even though the filming models for the whales may have been smaller to save a few bucks. If you see a Klingon Bird-of-Prey much larger than this, that would be K'Vort class. This one is B'rel class. They look the same only because the same filming model was used for both. The Oberth class has stated overall length of 120 meters, but the shuttlebay doors, etc. seem scaled to overall ship length of 160 meters. At 120, a Type 6 shuttle would have just a few inches of clearance. Scotty would have been standing on a catwalk near the top of the forward dorsal cargo bay. With those wrapaound doors (curved in two directions) open, large objects can be lowered in. And as far as seeing his feet, it would have been like standing in muddy water, using his judgment after having seen that space from below the cloak. If you look at a pair of slippers then turn off the light, stepping into them accurately is no problem. After loading, the tank was probably beamed to that lower deck. They wouldn't have bothered doing it the hard way.