Hmm, having read others' comments WRT the transport hulls, I've got an idea for you.
I tend to think that planet-to-planet transport of cargo (and even passengers) would be done with large modular cargo containers, INTO which individual companies' or private individuals' cargo containers are loaded.
If we assume a sort of "highport" affair for orbit-to-ground transfer of cargo, then the modules needn't even be capable of moving up and down the gravity well.
However, they might be small ships in their own right, in terms of STL, orbital-maneuver-speed movement. IOW, the actual transports might not DOCK to the local highport, they might simply pull up NEARBY, and let the Cargo Transport Modules ("CTM") themselves do the to-and-fro. If you assume one CTM per X kT of Transport hull-size, you get a built-in design lineage effect.
To make it a "containers on a deck" effect, Atrocities, you could have the raw Transports themselves have a large, flat area (a deck), with a half-hull section below it; the bow can be full-height, and come up to the level of the CTM's top. A bridge tower tothe rear, with the engines, gives you a pretty close concept to what you're trying to do. Configure the varying number of CTMs on that flat area, and you should have what you need.
For example, if you figure a CTM to be a big, hexagonal cylinder shape (with their own small bridge at one end and some tiny engines at the other), with it's length being 2x to 3x it's diameter, you could do (I assume one CTM per ~150kT of Transport hull):
TINY: Just a CTM (perhaps with slightly bigger engines), if such a hull size was needed (I think Neo or Neo++ uses Tiny Transports ... doesn't it?).
SMALL: two CTMs, parallel to ship axis, one beside the other.
MEDIUM: four CTMs, perpendicular to ship axis, in a row from bow to stern.
LARGE: six CTMs, parallel to ship axis; take the side-by-side pair of CTMs on the Small, put a third atop that (to make a trangle). Then place one triangle ahead of the other.
... and so on, if you want really BIG transports.
I think that'd give you a very "container ship" feel, and also something of a "wet navy in space" look, while being more "semirealistic SF".
You could even have the PORTRAITS be of transports
during loading/unloading ... nothing says a portrait has to be of the ship while in full flight!! Such a "mid-loading" portrait could help emphasise that the CTMs are semi-autonomous vehicles in their own right.
For the colony ship ... picture a one-CTM (parallel to spine) ship, where the CTM docks into a bay BELOW a domed area, like your image below has on it. Rather like the old transport / "flying crane" helo's, as far as teh CTM. Might tie the COL in to the Transport hull series, as a specialised transport of sorts.
Oh,and BTW ... those are some NICE-looking ships you've got there.
I can't wait for the finished product ... !!