Doubt it, because there are plenty of other workarounds to it. It's not worth the time and effort to start squashing them, when the current implementation has already cut down the queues to a fraction of what they were.
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There are still ways around the afk-kicker, more then one actually; a lot more.
If too many people circumvent the afk kick they will just implement the periodic full server logout again. Just logout if you are going to be afk for that long.
I was surprised when I found out FFXIV doesn't normally have an AFK timer. The only other game I've played that didn't boot you off the server for going AFK was GW1.
And nothing of value was lost.
I mean to be fair players can get around the timer. So yay I guess.
Remember when ShB launched and we had huge queues despite the auto-kick and Squenix was forced to boot everyone off the server during the night? Turns out the people circumventing the auto-kick were the actual problem and the queues dropped to a fraction of what they were. Looking forward for that happening again.