Is there a way to may the auto-relations use the origin as default instead of pre-existing geomerty that happens to be inline with the origin?
I am not sure what you are looking for, but when you are making a sketch, you can use the fully defined function and choose the origin as the reference to the geometry. See above image for selecting origin.
One way is to rotate your view in 3D so that you can see the origin offset from the sketch geometry.
Personally, I make every effort to minimize the relations to the origin. I usually make the first two pieces of geometry in a sketch be vertical and horizontal construction lines from the orign, then base all of the other dimensions and geometry off of them, not the origin. That makes it much easier to change planes later.
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