Some comments...
Some options should not be available at default. Here a TL-12 ship:
View attachment 5902
Neither TL-14 stealth, nor TL-16 armour should be available by default for a TL-12 ship.
You can have several drives, e.g. two different jump drives. See the Leviathan, HG p217.
The design system isn't a waterfall model, but a iterative method. E.g. we can't finalise the power plant, hence fuel tanks and crew, until weapons, screens, and sensors are installed.
Power plant fuel isn't correctly calculated?
If you default install power, fuel, and bridge, it is much easier to see how much space is required and left free.
Computers can be /bis and /fib.
A certain computer model is required to make the selected jump drive actually work. Don't present smaller computers by default?
There can be several different sensor packages installed. There are many other sensor options than the basic sensor package, it would be easier to select all of them in Step 7.
Weapon mounts can be left empty, e.g. a bay or barbette mount can take up space, but contain no weapon. A triple turret can contain less than three weapons.
Turret weapons take no space, only the turret takes space. A fully loaded triple turret is only 1 Dton.
Both turret weapons and the turret itself can consume power, e.g. a triple laser turret consumes 13 Power; four per weapon and one for the turret.
High Burn Thrusters are the same as Reaction Drives, they can go higher than 6 and take a percentage of the ship (and lots of fuel...)
Drop tanks do not consume space inside the hull, they are installed outside the hull, increasing the total tonnage of the ship, which affects drive performance.
It's not "200K Cr", it's "KCr200" or perhaps "200 KCr".
Many optional systems should probably be presented together in other steps, e.g. a detachable bridge is an alternative to a regular bridge, not an optional addition. Sensor options in the sensor step, accommodation options in the accommodation step a.s.o.
Docking Clamps allows carrying spacecraft outside the hull, increasing the total tonnage of the ship, which affects drive performance.
Crew: Commercial ships don't generally require a separate Captain, it can be one of the Officers or e.g. a Pilot.
Commercial ships require one officer per FULL 20 crew, i.e. crew/20, round down. The value can be 0.
Some crew positions are rounded up, some are rounded down, see examples in the ships. Generally Engineers are rounded up, and e.g. Administrators are rounded down...
There are no "single staterooms" and "double staterooms", only staterooms. They generally only berth one person, but can berth two people in a pinch.
Cargo: You can leave space unallocated as reserve for upgrades, so all available space should not necessarily be automatically allocated to cargo.
It's inconvenient to add small craft and vehicles in the Finalise step, after crew and accommodations are set, invalidating the design.
Some values might be more convenient as percentages, e.g. Staterooms as a percentage of crew and passengers, Common Areas as a percentage of total stateroom space, or Escape pods as percentage of carried crew and passengers. That way you don't have to redefine them everytime something changes.