Until then, they are just guessing in the dark.......
Now, knowing these two things, calculating fuel becomes easier. One can use the length contraction and the relativistic speed formulae to estimate fuel consumption. Better yet, instead of using relativistic speed, one can use a figure called "rapidity" for simpler energy calculations - it can be used to calculate proper acceleration (thus, thrust) in proper time.
The passage of time slows for the ship, as viewed by an outside observer. The people on the ship do not perceive anything unusual about their internal passage of time.
Don't conflate mass with time. They are two distinct concepts.
Physics can tell you *how* time slows at relativistic speeds. It slows by the Lorentz factor, 1/sqrt(1 - v^2/c^2).
Physics doesn't concern itself with *why* time slows at relativistic speeds. It suffices to say that it has been experimentally confirmed to be true. Leave it to the philosophers to ascribe meaning to it.
I think once the scientists figure out what causes gravity they will have a better idea how the universe works. Until then, they are just guessing in the dark.