I have notice such issue, and just built a Family premiun-ish testbed for 2 engines:
2.4L NA DI V6(rather reallistc)
2.4L NA DI V12(ridiculous)
the only tune for car is gear ratio
It seems V12 is better than V6, even the costs!
But in reality, no one would build such a V12 for famliy car…that has to be some reason… some penalty this game hasn’t implyed
Look at the table on the right, the V12 engined version has considerably higher production units and engineering time making it more expensive.
EDIT: it also doesnt look like you updated the car after you changed the engine since all of the stats are identical.
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As rcracer11m stated production units are significantly greater, in campaign mode that will be a factor for cost and time to complete each car making them more expensive, which will reduce the desireability.
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I also take severe offense to your implication that no one would buy a 2.4L V12 family car. Because I would buy the hell out of that, and I don’t even have a family.
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Only 6 kg heavier? Nice! (Scream you bastard!!!) 
Definitely not an issue right now, but something to keep an eye on for when we have it all in context in the LC V3!