Yeah, those choices mainly there to establish some of the morality of the main character, in order for the crew to respond to those choices. Refusing Thyia and Ziv for example will make it harder for Lilly to like you and get into a romantic relationship with you. The same goes for Ziv, if you're dismissive of Raene certain dialogue options and romance paths aren't available, because Ziv doesn't like you enough.
As for the instances where a character mentions something that didn't happen, those are likely bugs. Loading should reset the game state completely, it shouldn't retain any choices you've previously made using another saved game. So if you have any saved games of those situations, I'd very much like to check them out and fix any potential errors.
Both the itch.io and Steam version of the game use the same location for saves, so they should get picked up. The saved games are likely located here on Windows: Users\*name*\AppData\Roaming\RenPy\