I apologize, I may have misunderstood one of your previous posts. I thought you had said that you make no intermediate drawings. Now I gather that you do make some intermediate drawings.
However, even with intermediate drawings there is still no need to add features at the assembly level.
In the case of the part and BOM structure you've shown, I would:
1. Model the "Extrusion" as a base configuration
2. Add a part configuration for the "Cut" and model the cut
3. Add a part configuration for "Machined" and model the machining.
You now have one part file with three configurations. The "Extrusion" configuration has all features related to cutting and machining suppressed. The "Cut" configuration has all features related to the machining process suppressed. Now:
4. Add the part to a new assembly. Make sure the referenced config. for the part is "Cut"
5. Add a configuration to the assembly and call it "Machined".
6. Change the "Machined" configuration of the assembly to reference the "Machined" config. of the part.
You now have one assembly file with two configurations. The "Cut" configuration can be used to generate any drawings needed for the cutting process. The BOM structure will be indented 2 levels as you require. The "Machined" configuration is used in step:
7. Add this assembly to a new assembly. This is the final assembly to make your final drawing. The BOM structure will be indented 3 levels as you require.
Although this does add a couple of steps (adding configurations), it frees you from the constraints of the severely limited number of geometry-modification features available at the assembly level.