The issue isn't the decision. Had Thundercloud not procced in-queue, Thunder III would have likely been the WRONG decision. The issue is simply that it can proc in-queue, or alternatively, in the one event that there is NO decision between I, II, and III, that it should simply use the III rather than opening the player up to annoyances that has nothing to do with BLM decision-making.
The only decision would be, for someone counting server ticks in their head, dare I save .2 seconds of uptime by queuing, rather than letting latency affect my next spell, or should I wait for the server tick to see if I got the proc. And given the positive feedback on the reduced Firestarter delay, I doubt that was some job-favorite concept (praise it's humble birth as client information delay, and may it rest in peace).