According to that line from the wiki, this ship would cost 104MSP per year while supported by maintenance facilities, but would only use an average of less than 72MSP per year while deployed.
I'm not quite following, how do you get the 72 MSP number?
While the actual math may be slightly more complicated, the short answer is yes. It is possible to design a ship which is cheaper to run around for a few years and then overhaul rather than keeping it in port all the time.
So my understanding of the maintenance mechanic is that, when not being maintained in orbit, a ship will accumulate it's maintenance clock. When it gets back to port and enters overhaul it'll need to pay back any of the missed maintenance that's on the clock, so overhauling 1 year of maintenance clock will take 4 months (a third of the time), during which time it'll consume 4x the normal maintenance.
So, in case of a 416BP ship, after one year it has effectively 104MSP "on the clock". It enters overhaul and spends another 4 months in there until fully overhauled. During that time MSP drain is 4x regular, so 138.6. 34.6 of these MSP are consumed to maintain the ship for those four months and 104 are used to pay back the maintenance debt over the year.
Important to note here is that ships rewind their clock at 3x time, but pay MSP at 4x normal - because during the time they're in overhaul, they still have their regular upkeep on top of rewinding the clock.
Does that mean it is cheaper to keep a ship in deep space rather than over a colony if their MSP divided by Maint Life in years is greater than 1/4th their build cost?
I believe the confusion stems from this, the maint life of a ship does not have any bearing on it's upkeep cost, it only dictates the likelihood of maintenance failures while not being maintained, and any MSP cost incurred through those is seperate from upkeep aka. the maintenance clock.
...or I could be wrong about all of this and will be learning something new about Aurora today :-)
A slight further confusion is with regards to ships at a colony and under a training command. Since they suffer system failures, I assume they do not use MSP from the maintenance facilities. Is that accurate?
Yes, ships in training don't count for maintenance and shore leave even if in orbit. Ships in training run up their maintenance clock (and crew exhaustion) twice as fast as normal ships in space, so they actually consume double during training, plus maintenance checks.