Question: How was there a thunderstorm and rain inside the ship while traveling through space?
Answer: What scene are you referring to?
Question: Using the motion tracker with the screen when Dallas is in the vent, is it top-down or side-view?
Answer: It actually appears to orient both ways, presumably Lambert is switching back and forth between orientations. When Dallas turns; it shows on the readout as a 90 degree turn. When Dallas goes down the ladder the first time the readout shows the dot travelling downwards on the screen. It can't do both unless Lambert is switching them. And it makes sense that she would, she knows where he is because he is calling out his location as he goes. Lambert likely knows the path Dallas intends to take and switches orientations when he does. This confusing set-up is purposefully meant to disorient the audience, so they, like Dallas, have no idea from which direction the alien is coming. Lambert seems to have also become disoriented (this seems an impossible task with no line of sight) and can't give Dallas a direction to escape. She has the screen oriented so "forward" is to the right, Dallas goes down towards the alien, so she says "No! Not that way! The other way! God!"
Answer: That wasn't a "thunderstorm and rain" inside the Nostromo. It was condensation dripping down from the ship's ventilation/cooling system. When searching for the cat, Brett (played by Harry Dean Stanton) removes his cap and stands beneath a cooling shaft, allowing the condensation to splatter like rain on his head and face.
Charles Austin Miller