 Why is the air inside the machine not stale on the return trip like it had been on the prior trip?
Yes, it'll be pretty obvious it must be a time machine. You can see a sort of foggy nothing surrounding the cockpit; it is probably the field that prevents passage through time from affecting us. You are completely outside of time and space, as best you can guess how things are. "Maybe it's no dimension—or it might be the fifth; if you're going to skip over the so-called fourth without traveling along it, you'd need a fifth. Maybe there is no machine, and it's just easier for us to imagine it. Anyhow, you sit there, watching nothing all around you, and no time, apparently, though there is a time effect back in the luggage space. That means you either carry a small time field with you, or you are catching a small increment of time from the main field. You suddenly realize that everything in the machine is wide open, yet you haven't seen any effects of air loss. Out there is neither time nor space, apparently. You feel a dankish sort of air replace the stale air, and you breathe easier, though we're in complete darkness, except for the weak light in the machine, which always burns, and a few feet of rough dirty cement floor around. It gives out a coughing noise and the basement openings begin to click by us. There's no feeling of acceleration—some kind of false gravity they use in the future.
 Because there is only one Jerome smoking inside the machine.
 Because the generator is working and clearing the air.  Because there is a clearer air flow now with the retrieval of the generator.  Because no one is smoking inside the machine.  Because there is only one Jerome smoking inside the machine.