My questions (spoilers)

Are you asking because you turned this on mute with no captions and didn't have a lip reader available?

I try to answer your questions based on my perception, so I may be wrong.
1. The mission is to explore Titan, in quest of finding new source of energy for earth (methane)
2. I believe all that John saw, heard, felt are his hallucination or at least part of it,
side effect of the hibernation drug, so when the computer told John that he is alone, that's not true.
When Zoe told him that he is in simulation, that's not true. That's only in John's mind.
3. Fishburne character is captain Frank, and Nash is the flight engineer, and they are real.
Nash could also experience the hallucination side effect, and even worse than John.
4. Zoe is real, and what John experienced with her in the past (flashback on earth) could also be his hallucination or real, but it's not important. It serves as motivation for John to justify his hallucination.

I believe this because in the end you saw John was sucked up into the space. There is no point of showing this if John didn't hallucinate.

crew was hallucination. zoe was real. shoulda rolled credits when the airlock opened. definitive ending ruins the whole film.

he was gonna die no matter what. his stasis delusions were outta control. if it wasnt this thing it woulda been that thing. he wasnt ever getting home again.