The rebuy system just goes by the chip count as it registers, so if they have chips out on a bet that doesn't count. You're right that it shouldn't be allowed, but I'm sure the reason Party don't do anything about it is because it increases tournament prize pools and thus eventually their bottom line.
Question is more why you don't like it? I think it's a huge advantage having players do that. Like you say, their thinking is erroneous, because in your example they're not 'winning' an extra 3k like they think, they're paying for it. It just creates easier opportunities to pick up chips and a larger prize pool to boot. It does spike the variance having to show down more hands but it definitely creates more value, in much the same way more or less any kind of bad play from your opponents will. The majority of PP tourneys are freezeouts if it's not your thing, but I think there's way more value in the rebuys on there for these kinds of reasons.
"Morality is not the doctrine of how we may make ourselves happy, but how we may make ourselves worthy of happiness." - Immanuel Kant
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