First thing to understand is that APL covers a whole lot of different workflows, as well as being used by a whole lot of different user types and trades. So what works for one will not always work for another.
I think once you have your best workflow nailed down, you will find that points only showing up appropriately in different views is a good thing. But first we need to get that workflow figured out.
I will assume that at this time you have the point creation part down, whether manual, automated, or in family. If you have questions there feel free to toss them out, but for now I will not address that portion.
To get clean DXF's you are going to want to start by determining exactly what it is you want to see over on the magnet side. Lets assume for now it will be Walls, Pipes, and floors. Now most likely you only care about an outline of all of these. Look into creating a view template that is a floor plan with the visibility graphics set to only show those 3 things (And Generic models so the points show up). You would then use this view template to create floor plan views per level. For each view you would export a dxf and the points file. And you can continue to refine your view template and reuse it in new projects (Google transfer project standards -> view templates). Then, not including point creation, you will have a much simpler process per floor or area.
Last, I do realize that even with the above, you sometimes want to simplify the dxf even more. Simply put, the abilities to do such are in AutoCAD and not in Revit. So create the DXF from Revit, open it up over in AutoCAD, and take it through the APL DWG/DXF creation wizard, skipping any steps that dont make sense (Like Scaling).
Feel free to post followup questions.
Thanks,
Shayne Hamel
Manager, Principal Software Engineering