I'm playing a custom faction with Sheradyn affinity that I designed with the idea that I would use Dust as a main driver of production. I didn't take the trait that makes ships cheaper because ideally I shouldn't have to build very many of them. I'm not sure if this is wise or not, since I think that trait would affect upgrade costs. Anyway, I can confirm that at least under some circumstances it is cheaper to buy out a minimalist design and retrofit it to full capacity than it is to buy out the full design.
The Blammo is a basic Cruiser running mixed defenses and a complement of second tier kinetic weapons.
The original Blammo "shell" model just has a single weapon module and nothing else. Its production cost was 223.6 (in "Gears"); I was able to purchase it for 405 Dust (with the -30% Sheradyn affinity buyout discount).
The Blammo 2, with its defenses and fillout of armaments, has a production cost of 603 Gears. Cost to buy out production of one from scratch is 1398 Dust. I'm not sure why the Dust-to-Gears ratios differ for the two models; it may be that the discount for strategic resource abundance doesn't apply to buyouts. Even so I'm not sure that this would account for the difference — 1.8 for the shell vs 2.3 for the Blammo 2.
To retrofit a Blammo to a Blammo 2 cost me only 301 Dust. 405 + 301 = 706, roughly half of the price of buying out a Blammo 2. So at least under these conditions, it is indeed possible to save considerable Dust by retrofitting a shell craft.
One thing to note is that once you have upgraded a ship design you will be unable to add any more ships of the original design to your system production queues. However, any ships of that design already in the queues will stay there unless you use the button that appears at the bottom of the screen after you finalize your upgraded design. So you can add a bunch of them to your queues and just put them below a "convert production to Dust" item, for example, so they won't actually get built.