What occurs to me is that it is just poor accounting based on a factor in the original binary data based on the size category, shield strength, and so on, attempting to ensure that better ships scuttle for more. Whatever the original design decision may have been, it must have been poorly thought out, since it doesn't lead into gameplay as intended (a direct colony push) but instead into the construction of starbases that are never actually used.
For 1350 credits and 1000 titanium, the Cartare have an investment that yields ~7k credits and ~6k titanium in 12 turns after purchase at most. What's more, their starting transport will yield the payoff by turn 10, provided the second transport is purchased at turn 4, and none of this financial maneuvering requires labor, only one turn in the production queue. The painstaking effort of accumulating industry and mined goods in order to slowly crank out colony ships can all be bypassed, and colonies can all specialize in research, supercharging development for a race that is already strong.
Meanwhile the Omega Alliance doesn't start out with a transport, but a starbase that scuttles for 24k+ credits immediately on the second turn, with a comparable amount of saleable iridium. That is, while their outposts aren't nearly as profitable, they get payed in terms of titanium and credits much sooner.
Meanwhile no other race is remotely as good at starting development, having outposts that scuttle for about half the reward as the Catare, no starting transport to do construction, and no up-front payout like the Omega Alliance has. If the original design choice was as you suggest, then it goes a long way toward explaining the unbalancing effect of all these unintended consequences. Ships already take a lot of time to build as well as starbases, and scuttling a working vessel in tip-top shape should not come remotely close to the costs of the inputs required to produce them. The problematic gameplay emerges because it is trying to force ship scuttling to be close to profitable, and treating starbases as if the materials from their hull just appeared out of thin air, when in reality their fair scuttling value should not be much different from that of the transport which is the only material resource used to build them.