The 15 sec logout timer is the same amount of time an FSD charge would take. That is no coincidence. I propose that when a commander triggers the 15 sec logout timer the other commanders see his ship make a hyperspace jump (15 sec FSD charge and accompanying voice message). If they can't kill him during the 15 sec FSD charge they will think he jumped out. No problem.
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PS: Only if the FSD wake is scanned it reveals 'destination unknown' or so.
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--Ninja'd by Weps
The main difference in this situation is that if someone starts to charge FSD for high-wake, they can still have malfunctions that cause them to restart the high-wake; this has happened to me multiple times in PvP situations. The log-out timer saves you from any potential malfunctions.