I vote for the Fun Factor and GM fiat.
The first mention of a GG moon being inhabitable that I recall was Heinlein's Farmer in the Sky written in the early 50's for teens. Even then the terraforming of Ganymede required a heat shield of some sort to hold in the heat. That book had a Fun Factor when I was young.
Honestly, without the enjoyment of role playing and tweaked systems, 99.9% of the planets in any Traveller universe would be unihabitable, and the percentage of moons would be worse.
True, but the world-building rules in Traveller do very well at recreating the feel of Golden and Silver Age of SF. Since that's what I grew up reading, it made the game very attractive to me. Science has moved on since then, so anybody who wants a Traveller game set in an accurate-looking reflection of the universe as it's currently understood is going to have to do some major sysgen tweaking.
I do love older, less realistic settings for the space-opera feel of them. At this point they really have to be considered fantasy (sciencey-feeling fantasy, but fantasy nonetheless). It depends on my mood as to which approach I want to take- I can certainly be happy playing a science-fantasy sort of game if the background is interesting and reasonably self-consistent/true to its own internal logic.
Lately, I've been exploring rule tweaks to introduce more realism, just to see what happens. Most of the process has to be kept out of sight of the players; they get presented with the finished starmap and the UWPs and don't have to know anything about how things got generated.
But sometimes, you know, you just want to throw out all the constraints and explore the canals and ancient ruins on a Mars that never could have been.