The Jovian Chronicles rulebook has a chart to find flight durations between the planets. That table uses minimum, average (mean) and maximum distances between the planets (start point and end point of journey). The game assumes that the travelling ship is going “in a straight line” from A to B, pretty much ignoring the fact that the planets move along individual orbits and the distance between them constantly changes dramatically. It also has the prerequisite that your ship is able to constantly accelerate until midpoint, then turn around and decelerate. The cost or energy efficient way would be to take the long way following a Hohmann Transfer Orbit. On top of that any ship will have to adjust the flight path to the gravity of the planet where it starts at (even in high orbit) and the sun.
We could assume that most ships would use Hohmann Transfer and accept the much longer travel times. Only ships with time crucial missions would use constant burn to head directly towards their targes (rescue mission, military mission, fast courier mission). Especially transport ships would most likely use Hohmann Transfer Orbits. It all depends on the availability of propulsion technology and fuel/reaction mass.
Yet in Jovian Chronicles it seems that advanced drive technology and fuel are abundant and there is no need for long transfer orbits with short periods of thrust only.
This calculator is assuming that your vessel is going to accelerate constantly until midpoint (half of the travel distance), make a quick turnover maneuver and then decelerates at full thrust until it reaches it’s destination.
The calculator uses static distances between planets and ignores the fact, that they are constantly moving in relation to each other. In reality travel times would be higher due to the fact that the planets relative distance is constantly changing. For the outer planets this can make huge differences in travel time.
Calculating orbital transfer routes is much more complex. You can find some info and an example here.
It get’s even more complicated when you pass other orbits on your journey that an be used for a Hohmann-Transfer (slingshot) maneuver.