Glad to hear you liked it!
As for the Yes/No questions, I'm curious if you have some examples? Generally, most of the choices you make are tracked and could have an impact on how certain characters behave later on in the game. The choices you've made in Season 1 will carry over to Season 2 (and 3) and will likely play a role in the ongoing narrative. As for the crew selection, it's mostly a matter of efficiency over customization. Each different crew roster would mean a different story branch, so it would complicate development exponentially. My previous game (Sisterly Lust), had optional pregnancies and a customizable harem for the main characters (TFTUV will have this as well). Creating the different render variants for all those different pregnancy/harem configurations was an ordeal on its own.
That said, the core crew will not grow in numbers beyond Season 1. Also, if you don't want a romance or don't want to interact with certain characters, your dialogue choices will reduce their appearances to only the necessary story beats to advance the plot.
Season 1 automatically creates a special save game near the end. Season 2 allows you to continue with that saved game, in which case the choices you've made in the previous season will carry over. When Season 2 releases on Steam (or here), this will also be the way to continue your game. The main difference with the Steam release is that it has Steam achievements (itch.io version also has achievements, but they're local to the game) and cloud saves. Other than that the versions are identical.