I think first some caveats:
1) containers are going to be the top choice of moving cargo. Its efficient and allows for it to move from warehouse to warehouse before you have to crack the seals. So that's just like containers today (also allows them to be on truck and rail, or their 52nd century equivalent).
2) containers will be standard size. Large freight lines will most likely standardize on 5 and 10dton sized ones. They are well sized to move most items and are a good match as we've seen from terrestrial modern equivalents.
3) smaller freighters would handle the 5 ton ones, and maybe for smaller locations you'd get as small as 3 dton. That's reasonable sized to allow smaller ships to easily handle them.
4) space docks are going to have limited space to allow a ship to remove cargo if they need to get containers at the back. A good load master will load it in the order it would come off, but new cargo to be loaded can potentially fill up any spaces you just removed. So how to be able to access older cargo as you make your route (assuming you aren't point to point)?
5) stations will have limited surface space to allow for physical docks. So ship forms that are longer than they are wider, and load from the nose seem the best suited for space-only loads.
Right now the most efficient design I'm coming up with is a ship that stores containers in a rotary like mechanism, with the cargo in the outer rim and the center where crew, engineering and fuel are stored. Think of it like a ferris wheel, except cargo containers instead of people pods. Since traveller only counts internal hull displacement, the fact that you have a large circular portion with empty space in the middle, you don't lose any displacement volume to such a design - just what you have enclosed in the hull area.
1} I agree that containerization is going to be the top choice (for non-bulk cargoes) for big players in cargo handling. The 'do not need to break the seals outside a warehouse' aspect is pretty important; and it means that cargo-handling equipment can be designed to standardized specifications to handle containers, or groups of containers.
2} I agree that containers will be in a small number of standard sizes; and probably will only differ in one dimension to maximize compatibility. I tend to think 3m x 3m containers make sense; other folk might have different visions for their own TU.
3} Small ships will handle small containers, if they handle containers at all; more often the player-scale ships are picking up scraps (left behind by the big fish) that are not containerized for various reasons. A tramp free trader is more likely to pick up palletized or crated cargo.
4} A load-master will obviously try to arrange cargo aboard such that the cargo next to the loading/unloading hatch is tagged to be unloaded at the next port. Big cargo ships will be able to manipulate their own cargo inside their cargo bays -- but full bays leave no room for shuffling things around. The solution might be to load the cargo as cubes, where any cube can take the place of any other, and moving any cube creates a space for another cube to move into. Think of a 'Mystic Square' or '15 puzzle' style cargo arrangement.
https://en.wikipedia.org/wiki/15_Puzzle Once all of the Cargo is properly arranged, the last vacant space (the 'Magic Cube') may be filled in with cargo going to the very next port.
5} High-ports will have limited volume for mucking about with cargo, so ships will be loading and unloading as close as practical to the warehouse -- sometimes directly into a warehouse. The ship will nose into the dock & immediately unload the block nearest the door; which will create enough space to manipulate the remaining cargo to reach whatever else needs to come out. Any 'partial' blocks will be combined as much as possible; sometimes empty containers can be used to complete a block if it only a little short; any cargo which does not make up a reasonable portion of a block will be left for spot-market carriers.
I am envisioning a mega-freighter with one to three stacks, of 2 or 3 (each quite long) parallel lines, of cubes. The cube next to the hatch is the 'magic cube' -- first unloaded (then cargo shuffled) and last (after cargo shuffling) loaded.