In the first one, the components would come on arrival. The ship would have to come later, because it's a home and it sounds big. In the second one, it would have to come later, because it's a home and it sounds big. (This goes for Macross-class ships that turn into giant-giant mecha, too.)
The current rule definitely does give ship-people a small disadvantage at the beginning -- people with fighters get the morale boost of "hey my robot came with me!" when they arrive, and people with ships don't. But remember that the fighters don't function until the pilot has saved up five quartz for them, at which point the fighter regains basic functionality. With ships, it will cost more to save up for them (tentatively it'll be size proportional -- a 20 meter fighter takes five quartz to power, so a 100 meter ship takes twenty-five quartz to pull through the Clamshell), but they'll come through the Clamshell already having basic functionality. Now that I think about it, the "when your ship gets here, it will be working" isn't on the page about trade-ins and I should add it. So the disadvantage ends at the time of trade-in.
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The current rule definitely does give ship-people a small disadvantage at the beginning -- people with fighters get the morale boost of "hey my robot came with me!" when they arrive, and people with ships don't. But remember that the fighters don't function until the pilot has saved up five quartz for them, at which point the fighter regains basic functionality. With ships, it will cost more to save up for them (tentatively it'll be size proportional -- a 20 meter fighter takes five quartz to power, so a 100 meter ship takes twenty-five quartz to pull through the Clamshell), but they'll come through the Clamshell already having basic functionality. Now that I think about it, the "when your ship gets here, it will be working" isn't on the page about trade-ins and I should add it. So the disadvantage ends at the time of trade-in.