Many a times I book a ticket in 1039 Maharashtra Exp from Ghorpuri to Akola, boarding Pune. Even if the ticket is WL from Pune, I get confirmed ticket from Ghorpuri, but Pune as boarding station. This proves that the quota used is that of ticket starting station, not boarding station.
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This is how it happens in Mumbai-PRS trains. However this is not the logic in other PRS trains.