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Now as the .screen windowing system is explicitly not designed to deal with overlapping windows, so this probably won't be resolved by being able to bring a window to the front or similar. Now the solution that springs to mind is to make the crafting queue physically smaller so it interferes way less. Looking at the styles, I seemed to succeed at first, as the crafting queue buttons have their own style ("crafting_queue_slot"):
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However, as you can see, the up-arrow-button to expand the crafting queue is not influenced by this. This is because it uses the pretty general "slot_button" style that a ton of other buttons use. So you can't change that without significant side effects. The solution I propose is to give that button a custom style, that just has "slot_button" as it's parent. This wouldn't change anything for the base game, but allow modders to change it's style.
Again, I'm sorry for this, it's stupid, but I'd really appreciate it.