The truth is there never was a straight boat to start with, last chapter Kouta confessed Nagisa was precious even before OTMS happened, the straight boat was never even built let alone sunk.
As I said above Kouta found Nagisa precious even before OTMS(so when both were always male bodied at all times). Just didnt have the courage/knowledge to say so back then.
So it is true, this goes beyond physical bodies and just leaves us with love of a person.
I honestly don't think you understand the the power of attractiveness. It can literally start wars and end empires and whole dynasties.
Kouta only ever saw Nagisa as a romantic partner only when he was put to the wall that Nagisa would be a attractive girl forever.
If gender bender manga didn't turn every male character that is a 4 out of 10 into a 9 out of 10 girl, then no one would ever stick to reading the manga.
A straight gender bender pairing I think is done perfectly in the Heavenly Disillusion manga when the man turned full woman has to not only come to realization of their new bodies and lives but also the problems that come with it.
Someone also pointed out Boku Girl, yes that is true, but it also doesn't go as far as Heavenly Disillusion did.