Gosh, yeah, out of gas. Of course. "We're dead in the water... Main life support is down on account of engine being dead... Engine don't turn, life support won't function, we don't breathe." That would certainly imply that the power supply and main engines are integrated, though presumably it doesn't only provide power while the ship is engaging in pulse-drive maneuvers.
I think, mechanically speaking, it still works okay to treat them as separate systems in a write-up so that it's clear what the tonnage, cost and output of the engine's power production components is in Traveller terms. Might get a little tricky otherwise. It would all be combined on a map though and you might maybe have some crossover when it comes to the crit tables.