Matthew,
I think you are seeing two issues here.
One is the different configurations of the assembly, and one is the configuration of parts.
Assembly: You need to do this in two distinct steps.
Step one would be the weldment of 2 or more parts, and subsequent drawing detail (no holes, no machining).
Step two would be to create a derived part of the weldment, and do the holes and machining on the new ‘part’ (which is actually a weldment). You can then create a drawing of the new part, with the machining detail.
Part only: In my experience, you are best to do this in two steps also (for flame cut, then machined parts).
Step one- Create the part with the profiled hole (which is smaller than the machined hole will be), but do not create any drilled holes. Then create a ‘Profile’ drawing, from which you can export the dxf easily etc.
Step two- Make a new derived part from the ‘profile’ part and do all the machining and hole features. You will be able to have another drawing now, with the machined details.
With solid modelling, you are generally best to design the part exactly how they would do it in manufacture. Both the process above simulate that. i.e. when the welder completes his (or her!) task, the assembly essentially becomes one part for the machining process.
I hope this helps, but I am sure others will have differing opinions
Hayden