Some cargo bays are indeed multideck. The Subsidised Merchant is a common example.
That is contra-indicated by the description:
"In fact, if its cargo bay doors were larger, the subsidised merchant could theoretically swallow a free trader whole."
HG p189
The Type P Corsair on p195
"is infamous for devouring 100 ton ships whole and delivering them to criminal starports for refurbishing into ships that cannot be identified as the originals."
I do not believe that any 100T ship is only 2.5m in overall height (since they are at least one deck high internally themselves.
MGT2 deck plans are not necessarily consistent with the description. The corsair for example has a 220 square docking space. that must equal 110 tons of open space and each square is shown as 1/2 DTon. It does not say that each square is 1.5m on a side (though that is the conventional size and is consistent with staterooms for example). They could for example be 1m on a side and the deck height for the corsair could be 7m. This would make the other compartments oddly shaped and likely impractical.
I was specifically sticking with the Air/Raft earlier, because there is a practical minimum ceiling height, and getting in and out of even a small vehicle is going to need that (call it 2m, which is headroom for a tall human or average Aslan). The smaller vehicles are going to be less efficient in terms of bay dimensions; and I'd distinguish between vehicles and small craft here.
Except the rules do not distinguish between small craft and vehicles. HG p61 has:
"This is an internal bay in which a smaller auxiliary ship or vehicle can dock."
Small craft are often shown snugly mated to the ship in an open cavity (the Broadsword cutters are a prime example). Because the small craft is spaceworthy, this doesn't cause any big issues and you can set up an access point for when they are docked - you just open the ship hatch, open the craft hatch and board.
The Mercenary Cruiser cutter wells are not actually docking spaces per the description in HG as they are external to the ship if we are to believe the deck plans. They would be better described as docking clamps. It would be far more efficient to use docking clamps as the cruiser isn't streamlined (ditto the laboratory ship). This is a prime exemplar of the need to use common sense as the mercenary cruiser pre-dates the introduction of docking clamps. Someone drew a "cool looking" ship and added the components available at the time that best matched that concept. They are also not shown on the graphic of the ship as being external (or indeed present).
The images are not blueprints, they are artists impressions and not necessarily to scale and as we have seen in other publications even if they were, size is somewhat fuzzy. Frankly the deck plans of the cruiser bear no relation to the supposed spherical shape of the ship. It looks like the ship should actually be cylindrical with bulge around deck 3. It looks like the walls of the ship have been omitted from most of the decks to save space, which isn't helpful.
The air raft is also space worthy (you just need vacc suits) and is explicitly described as being capable of reaching orbit. Things like the ATV are deemed to have an exterior hatch. Most other docking spaces are fully internal (with maybe just a bubble canopy or roller door separating them from space).
That's not usually how a vehicle bay needs to work. Nor is it practical to move a vehicle out into space to repair it in most cases.
In which case you need to allocate twice the volume as it requires a hangar. I'd be happy with a 4 DTon hangar for air rafts but that is not consistent with the RAW.