I just finished a game where I saved Cossette but scrapped her Ryder. I didn't get any cut-scene with her at the end of the game whatsoever. I was kind of expecting to see her face pressed up against the window at the very end complaining about being forgotten. I think I would have had 4 affection with her normally, but this time it was zero affection. So by scrapping her Ryder you lose all the affection gained from previous choices.
Thank you for your contribution to science! With your help our collective knowledge has increased and made us that much more powerful. Just a bit more and we might just be able to take over the world.
It would make sense that trapping Cosette and then leaving her Ryder to rust in the hanger bay would piss her off. Still, it is kinda weird that it didn't get tossed or completely scrapped for parts when the decision was made. I guess that is what Kayto gets for being lax on his Ryder Disposal paperwork forms.
As an engineer, let me tell you it's not totally safe. It's safe enough that it's not cost-beneficial to make it safer.
Apart from stating the obvious, my impression was Cosette was a completely forgotten character in LD and RT. Even if all of the choices made in both the games were in line with her affinity, her appearance is barely a cameo, and in the final mission when she does re-appear, it's in a very short battle that can be bulldozed through in just a few turns even on harder difficulty settings.