Playing "angel's advocate" (I guess):
1) In an Apocalypse setting, why would any women want to have sex with a tentacle monster? Why wouldn't the initial reaction from the survivors be 'kill it'? Why wouldn't a sentient creature want to know where it came from let alone what is its purpose?
1A: Perhaps it has saved her life from something worse and is able to talk, thus, over time, building a romantic relationship?
1B: Perhaps the tentacle monsters appeared
later, not the cause of the apocalypse just a side effect, like a RIFTS type situation for example?
1C: Who says they don't 'want to' that doesn't mean they DO: the 'why are we here' question has bedeviled humans since the beginning of time, why should the tentacle monsters be any different?
2) If tentacle monsters are considered pure evil why would any woman want to have sex with it? Surely it would be hunted continually and thus back to being a rape monster? And if it has to use female humanoids as hosts I imagine the punishment to the woman, in the fantasy setting, would be death?
2A: Perhaps the woman in question has the ability to sense 'evil' much like a D&D Paladin, and ergo sensing that this tentacle monster
isn't evil, desires to propagate this superior trait, (from her perspective,) among the species?
2B: Maybe, or, going back to the previous reason, the woman has the power/authority to declare this specific one an exception? Sort of like a presidential pardon?
2c: Maybe, but this is a fantasy setting, depending on the cultural basis and amount of magic commonly available their attitudes might be more enlightened, knowing that the woman had no choice in the matter and as such was blameless. (I point to an existing example of such as fantasy setting in the 'Valdamar' series by Mercedes Lackie.)
3) Why are they together on a ship? If they are both known sentient aliens why haven't these factors been approached in the past?
3A: Three ideas spring to mind Immediately:
I: They are an experiment by their respective governments in such mixed-race missions. This allows for conflict with both races being shocked and appalled by the interspecies romance.
II: Wheels of Circumstance: the two of them were thrown together by chance, such as each having
half the funds needed to purchase their ship. This opens possibilities of the two of them questioning why fate has thrown them together as the romance deepens...
III: First Contact: The tentacle monster or the human was rescued by a scout ship of the other species after being found alone in a damaged derelict in suspended animation...
3B: As for why they haven't been approached, this is very simple: there must be a first time for everything and these two 'drew the short straw', so to speak.
Of the three the third idea sounds most plausible. The tentacle monster is a sentient alien race, one amongst hundreds, and is known. Think of a Star Trek-like situation, where one of the crewmen is the titular 'tentacle monster'. You are then exploring the protagonist's sexual viewpoints, developing its relationships with the mostly human crew which are mostly unaware of the 'new' species to have joined their ship allowing you a platform to explain things in the scene. If you want to throw in the occasional 'tentacle monster rape' then there are countless ways to have it lose control without it then being flushed out of an airlock for the crime, even then exploring its feelings towards those actions. Especially if the race does have some primal 'fuck all holes' emotions that the civilized and sentient tentacled species have to suppress, or the race still has a very 'non-consensual' attitude towards sex within the species.
Something to consider in this last sentence: humans are VERY unusual even on Earth in that mating involves consent at all, take a look at the common housecat, not only does the female not enjoy sex, it's in fact incredibly painful, and this is a necessary part of the mating process for that species...
1) I didn't actually say that 100% consensual branch is guaranteed. Yet there are other ways besides straightforward rape. Something like providing food and protection for sex that may develop in some kind of other relationships. They need a way to communicate, but this is solvable.
1A: I find your lack of commitment to this concept troubling.
1B/C: Protection, Companionship, and Shelter are also things the Tentacle Monster could provide to win the woman over.
1D: That's easily solvable, it's your story, just say the tentacle monster can talk and you're
done.
2) Well, there are many ways to start a consensual route. Even something simple like a wounded female warrior being 'attacked' by the monster only to be healed and not touched because this one has different ideas about the acceptability of rape. As for why full extermination doesn't happen... It is not that easy if they live somewhere like Amazon forests.
2A&B: A tentacle monster cleric could be an interesting concept: it also could neatly explain why it's not evil, it had a religious conversion and changed its life.
2C&D: There are also several other environments that could make such a campaign difficult: aquatic, subterranean, swamps/marshes, and forested mountains to name but a few.
3) Actually my idea here that "tentacle monster" aliens aren't usually interested in other species. As for why they are on one ship? They live in an empire\federation\republic that spans over many star systems and has many citizens. Why can't they start cooperating?
3: This seems like a perfect solution to me, something vaguely like the Star Wars galaxy, or the Buck Godot universe.