I would be happy if clicking "commence" just put your character back in the same state it was in when you entered the queue and overrides things like open transaction windows, market boards, cuscenes. etc. I've missed a queue before because I was frantically trying to exit out of my retainer, enter my character window, and change my job back. If I'm only on a controller, this is a real pain, one miss-click can really cost you precious seconds.
EDIT to add in other ideas:
That is a valid point. So instead of putting you in the same state you queued in, how about just auto-equipping the gear set you queued with. If you made changes to that gearset, as long as you updated it, it would be fine. Not sure if this "solves" the problem but my solution was more for people who just want to make sure they get in, of course you still have the timer to make other adjustments before clicking commence. Ah! or have a third button that provides this option? "Commence" "Quick Commence" "Withdraw"?
Since I've seen a few people say this I would like to respond. That works fine if you are just looking through an options menu and i'm not saying i'm always in this situation. As for hotbarring a gearset, i already have 4 hotbars that are full on my main Job. I really dont want to add another one just for this.
Exiting out of your retainer takes a bit longer, you have to wait for them to say goodby, then disappear, and in the process you also close down your duty queue, unless you start adding in more buttons like select. if the queue closes, you still have to equip your gear, then open the duty window, go to the bottom, and enter it.
I'm lucky that most times I have my mouse and keyboard handy so I can click on windows which makes things easier, but there are so many reasons that a longer queue and/or a secondary button would aid things immensely. especially with such harsh penalties, I don't think as many people were abusing it as people think.