I want to preface this with a disclaimer of sorts. We're splitting hairs...if someone next to you(or near you) on the flight has COVID and you're not wearing a mask you're probably going to get it. Despite our disagreements about the minutiae of flying I'm pretty sure we all agree on that and wish there were better data.
So, I came to a different conclusion than you did, now having read it, from that very small sample size!
It's actually way *less* safe than the model that everyone uses showing a 1/1000 chance of contracting COVID on a plane. This study is suggesting transmission during the flight(when HEPA filtration should be a thing) across 4 rows, and with mask and glove wearing:
"passengers A, B, D, F, and G self-reported mask and glove use while on the airplane but passengers C and E did not"
That insinuates that even wearing a mask you could be infected on a flight from at least 4 rows away. As you pointed out, 18 hours is a long time to wear a mask without taking it off to eat or drink, so it's likely that they did take their masks off at some point, even briefly.
I keyed in on the 2 hour refueling stop in which no one left the plane.
"No passengers entered or exited the aircraft during the 2-hour refueling period in Kuala Lumpur."
I assume that's like sitting on the runway in which the HEPA filters aren't running? But I honestly don't know, so I'm going to leave that aside for the moment in my analysis.
One limitation is that I don't see a discussion of the time the plane spent on the runway, was it delayed and sat for a while, etc. I think that would have been a great data point as that's almost certainly the most dangerous time for a more "normal" shorter flight. But, again, we're talking a study on a single flight with 86 passengers and 7 positive tests. It's the definition of small sample size.