Have I missed something else in the book? I confess I haven't gotten through it all. (for instance I haven't read details on the orbital weapons yet)
The Colony Ship Framework feature is basically:
For an extra 1/4 the cost of a Large, or larger framed ship, you can make it a colony ship. Support 10x the max crew size from a habitability standpoint. Triple the number of expansion bays, but the additional ones, can only be used for civilian purposes. Additionally, it gets a discount for adding one orbital weapon on it.
Unlike the Space Station Framework, which clearly hurts the pilot check, maneuverability (-1 pilot, turn 3), and speed is quartered, round down, there is no mention of any impact to the maneuverability, speed or other limitations to the Colony Ship. (other than limitation on what you can do with the extra expansion bays you get)
It seems like some sort of limitation, or drawback should probably exist other than a probably minimal BP cost to modify the frame (and extra BP to populate bays).
What would for instance stop you from taking a Bulk Freighter
Lets say a Hivonyx Titan Hauler design as a basis, and make it a colony ship framework. It now how 20 extra expansion bays, which we will simply fill in with cargo bays, which are 0 PCU/0 BP , or use some of them for Passenger seating if you can sell seats ferrying people with this thing. It would go from having 5 cargo bays, to having 25 of them. For the cost of perhaps half of a tier's worth of BP
Or just compare the frames as a base. A heavy Freighter frame with the Colony Ship Framework, give you better maneuverability, cheaper defenses and engines, and gives you 24 expansion bays, vs 10 if you'd paid 5 more to get the bulk freighter frame. (Granted the Bulk Freighter frame doesn't insist that you have 2 civilian expansion bays, but I suspect most Freighter frames you are considering this will want at least 2 cargo bays, so that won't really be a significant limitation.
Was it intended to only have the minor limitation of costing a little more, or was it supposed to impact the speed of the craft and/or other things such as cost of armor/defenses/shields and such?
Considering that those extra expansion bays are almost entirely flavor, and add nothing to the ship's abilities in combat, I assume it was intended to be cheap and with few downsides.
I believe the space station framework has the limitations it does primarily because it is a space station, and therefore not supposed to be mobile.
In a game like Traveller where you might need to make a profit with your banged-up freighter to keep it running this'd be unbalanced. Starfinder is not that game.
While I suppose there were quite a few people who pointed out that Starfinder's strong points was not in its game economics, that might have seemed a reasonable assumption that players wouldn't play a game like that.
However, given that Paizo published some rules that involve just that (Galactic Trade rules), then it seems that you would likely agree that that option would seem unbalanced, with no appropriate trade-off for making the choice, if players can get ahold of other ships and use them as part of their trade empire. Was that the intent?
Would that mean that you have to Gate the Colony Ship and Space Station frameworks as GMPC only options? Although an option, not at all my preferred answer. Do you think that there was intended to be some other trade of (half speed, instead of quarter like the space station one, and/or pushing the maneuverability class of the craft down one (minimum of: Clumsy -2/turn 4) or add one or more to the turn distance. External expansion bays for instance increase the shares/turn by 1 each three bays.
Other options what if all features who's cost is based on size category would cost 2x as much if you used 2x the base number of expansion bays. Or 3x as much if you used 3x the base number of expansion bays.
For more of a backwards compatibility, you could allow the BP used to pay for the framework to pay for the extra cost (but not the standard/base BP cost for the armor)
But really I'm more interested in knowing if there was something that was missed, as a side effect of having chosen the framework, and it got edited out for space or something like that?
Having taken a look at those rules now, you're unlikely to often have so much cargo that you need a colony ship to transport it. Different cargos may sell in different places or have incompatible complications. As a GM, if using those rules make different cargo lots need to be sold in different places and you remove the incentive to get 10 cargo holds. THe PCs can then use a colony ship to have cargo holds and interesting expansion bays.
That all works, except for the annoying way that BP and cash totally fail to interact, which this highlights but doesn't/can't alleviate.
I'll be honest, even with those trade rules the colony ship's extra cargo doesn't sound problematic even at it's low cost. If anything, I'd just increase the minimum crew requirements, and add in a 'pay hired crew members' as another way to spend BP.