[whpalmer4]

I'm not an Omni Ninja, but I'm fairly confident that they won't disagree with me saying that what you are describing is the way the product is currently designed to work.

Why not just turn off the due soon/overdue notifications in the sidebar and dock if they give you that much stress? Make a perspective to show you the due soon and/or overdue items, and consult it as often as necessary.

If all your projects are filed either in the work or home folders, you could try marking the other folder as dropped when you start work in one place, then flip it back when you go to the other...