I’m fairly certain that what we hear on the record is cut from a much longer recording and it maintains some granular delay and tons of reverb from the parts we do not hear. So I’d say it’s a 100% wet signal that we are hearing the long tails of. Then the foreground melody is also heavily processed very likely through a modulation model we sorts. The Line 6 MM4 can emulate a Leslie speaker (the one where the cone spins around) and something like that could get you there once you have the tambre of the ‘organ’ patch in hand. Remember that Trent Reznor is extremely experimental so if that melody was made with samples of the reverb tails of the whole textural background in key and then put through a resonant filter that would not be out of character for him at all.
Just gonna give it to you exactly like it is.
Download some samples pop then into your DAW, have fun!
Build on that for a bit. Chuck it and start a new one if it feels like you are forcing it/getting demotivated.
Once you have something you like it will probably be waaaay too much of everything so start removing parts, see you that starts a progression/arrangement and follow that until you reach a point.
Slowly start making your own samples, maybe pick up some gear to make your own loops with. Fall in love with a synthesiser.
Don’t pressure yourself, just enjoy being creative and make something you like.
No sweat, have fun making music!