On a basic level, the difference in lifespan is due to the fact that the nautilus has a vastly different reproduction strategy from other living cephalopods. While most other cephalopods exhibit a rather extreme form of r-Strategy reproduction, the nautilus is, relatively speaking, a K-Strategist. To explain, r-Strategy is when a species produces many offspring, but puts relatively little investment into each one under the expectation that most will die. K-Strategy, on the other hand, produces relatively few offspring, but put much greater investment into each one.
As you stated, in most cephalopods, sexual maturity triggers a shutdown of the digestive tract, as they put all their energy into reproduction, during which one spawning episode will result in hundreds or thousands of eggs. After fertilizing the eggs for males, and for females after laying those eggs (allowing for a delay of a relatively short incubation period in some species, including most or all varieties of octopus), the adults die, having produced enough young to guarantee the next generation. This lifestyle of a single massive reproduction event before dying is called semelparity.
However, with nautiluses, each mating results in only about a dozen eggs. These eggs are much larger than the eggs of any other cephalopod, have a considerably longer incubation perios, and by extension, the hatchlings start out larger and better-developed. However, technically, nautiluses aren't true K-Strategists, like humans or whales, which have only one offspring at a time and put a massive amount of investment into that offspring. Instead, they are more like cats or dogs, Median Strategists, who fall somewhere between the extremes. While for r-Strategists like other cephalopods, semelparity can produce enough young to ensure the survival of the species, this is not the case for Median or K-Strategists. Instead, they must reproduce multiple times over the course of their life, a strategy called iteroparity.
While in all cephalopods, the gonads are destroyed by the process of reproduction, in nautilus females, the gonads regenerate after spawning, allowing them to mate again the next year.
It should also be noted that despite this, the nautilus spends a relatively small portion of its life sexually mature. It takes roughly fifteen years for a nautilus to reach breeding age.
While my knowledge of genetic engineering is pretty much limited to what appears in the news, based on this information, it seems like to lengthen the lifespan of other cephalopods to be on par with that of a nautilus, you'd have to completely change the way they reproduce and the rate at which they mature, which I tend to suspect is beyond our current abilities.