I would hope so too and, nothing personally, hopefully they could look for the pros and cons in, not just your ideas, but those of any put forward.
Back to case in point, 45 seconds for a load screen, since you did specifically mention it several times, is just beyond necessary. If someone is having hardware issues that is causing a load screen to be that long, what would they be like in Titan? That's going to hinder the party. I'm not exactly running a modern PC, it would be very low end but it gets the job done, relatively longer load screens than others that I play with but by no means would it be 45 seconds.
As for those crafting, watching cutscenes, if you are too busy to get your stuff done in 45 seconds to press commence, then you're too busy for a dungeon. It's all about priorities. Sure the system isn't optimal for everybody but as of right now, it works and it works well. As much as people love to misuse the word 'broken', this is one of the things that works well. Queues times are not down to SE, it's down to player choice. If a player choose to craft or chooses to watch a cutscene while another players chooses to be available to press commence, fair play to them. Let them enjoy the content they queued for.
As for tracking each individual player's inputs to determine if they are or are no eligible for a pause status on their DF queue is just absurd. This would involve invasive programming to see what inputs a player has on their computer because I commonly tab out for longer periods of time and have my audio running in the background so I can listen for my DF pop, the game could have no inputs for a long time but I am still here. Or yet, I could be afk and using wireless headphones, which I do, to listen for my DF queue. Same issue again, no inputs over an extended period of time but I press commence. Yes, it could go back to what you say and look at a particular player's history of if they do or do not press commence but a player should be ready to press commence anyway, regardless of their history. As a tank, since most things are instant queues, why should I reserve the rights to be afk over anyone else? I say that because of my instant queues, I am more likely to be here, ready to press commence over aDPS who is afk.