It won't affect anything since SE gives you the needed targets during those quest to activate those skills needed to finish those quests.
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Not only are you able to turn off the battle affects of others (even party members and yourself!) but you can also turn off the sound effects of other players, too!
Now I have this compulsion to run around Idyllshire and spam Ring of Thorns.
RIP SMN/SCHs who pre summon their pet when their queue pops
While I find it annoying to see whm and drg spam their moves over and over for the purpose to annoy people or because they are THAT bored. Disabling abilities in towns is a bad idea. If it annoys you that much you can just turn off sounds/effects in your window.
Correct me if I"m wrong, but would these cases held in an instance...away from other players. It seems likely that they wouldput the few that are set in the server proper in an instance and just disable the skills in Towns (and Iddylshire).
I could care less about this but I felt like pointing out that SE can find ways to implement with without changing the quests if they wanted to.
https://www.youtube.com/watch?v=ZpWvNI4J7pM
Every time I'm crafting. Every. Time. Must. Not. KILL.