The Derived Part method is usually my preferred technique for this sort of situation. However, we've been tinkering with another method. May not apply to your situation, but I think it has a lot of potential for us, so I mention it here just in case it would help you.
Our nesting software (SigmaNEST) has the ability to directly import Inventor part files, so we don't have to export a DXF or any other neutral format. A few months ago, we discovered an option in the nesting software called "Use Feature Mask". If we turn this on, then enter some text, we can then cause features that begin with that text to be ignored. So we can name the machined cut features beginning with "MACHINED-" or some other such tag, and it will be ignored automatically by the nesting software. We haven't used it on anything real yet, and haven't settled on a standard feature name tag, but it looks promising. I don't know how well it would hold up to large differences in profile - my brief testing revolved mostly around using it to ignore drilled & tapped holes.
We are able to import the assembly and automatically generate the proper quantities of parts to be burned. Because of this, the Derived Part method doesn't always work out well for our shop guys, as it's the finish-machined version that would be in the assembly. I've performed all sorts of hokey tricks to try to get around this (weird BOM settings, actually naming files things like "PL-02 Finish Machined DO NOT BURN" and "PL-02 BURN ME", and so forth). Sometimes my nonsense works, sometimes it still gets burned wrong.
Although I'm a fan of the Derive method because it closely follows the real-world manufacturing process, this nesting software option may be a better solution for us to make sure the right geometry makes its way to the table. Assuming, of course, that I can someday get enough of a break in day-to-day work to sit down with the table operator and settle on if (and exactly how) we want to use it.
