Yeah, I've seen those before. It does seem wierd at first glance.
In the case of real-time, it could be that even though they were winning, they literally ran out of time to think about what next. Or it could be that some real time interruption occurred for them. EG they got called to dinner or whatever. I don't know what you can do about this. Maybe the fact is that if you time out you lost. As simple as that, It's part of "how good you are" IE your rank is not only how good you are at placing stones, but how good you are at finishing games.
I see now why someone might get an unexpected boost though: if you are playing someone who outranks you, and they time out, then you will get quite a boost even though you might not have been able to actually beat them.
But still - to be fair in this case you'd have to assess whether the lesser player actually was winning and thus the cause of the timeout was the higher ranked player running away. If that was the cause, the lesser player would deserve the boost.
This all gets too hard: it's much easier to treat a timeout as an actual loss, but also punish timing out more than we do here in OGS. Most conversations about timeout seem to end in the OGS concensus being that it is not a sin. But look at the trouble it causes...