Although I do design a lot of sheet metal parts on a regular basis in Inventor, I rarely need to create flat patterns for them for CNC purposes, because we usually have other companies fabricate them for us. I do not actually use MarkFeatures that much myself either, but understand them pretty well. If you have not already done so, you should probably look into the MarkStyle objects used when creating MarkFeatures. They seem to contain a lot of useful sounding properties and methods which you could probably make good use of, and may even want to create some custom MarkStyles with those settings the way you want them. One of the most important properties of a MarkStyle is its MarkStyle.MarkDepthType property, which is Read/Write and has a MarkTypeEnum type value. That is what determines if the mark just marks the first surface it comes to, or if it goes all the way through the part. And since it is possible for a mark feature to only effect one side of the material, or effect both sides, there are lots of settings for the 'layer' being used for that geometry on one side, independently of the other side, with their own line type, line weight, line color, and so on. I'm not sure how well that model data carries over into a view of the flat pattern within a drawing document though. Since drawing documents do use layers, where model documents generally do not, plus we can include annotations, such as bend lines/notes, it would seem like exporting the flat pattern from the drawing, instead of directly from the model, might have more options for customizing the layers though.
When exporting a sheet metal flat pattern directly from the model, about the best way to do so is like the following:
While in the flat pattern editing mode, right-click on the main flat pattern node in the model browser tree, then choose 'Save Copy As...'. That shows a file dialog for you to specify the file name and location, but the 'Options' button is greyed out. However, once you specify the name and location, then click the OK button on that dialog, a second dialog shows, labeled 'Flat Pattern DXF Export Options', which is very intuitive, and has lots of settings & options spread out across 3 different tabs. One of those tabs is for customizing the Layers. And when your flat pattern includes mark feature geometry, there are usually at least two additional layers listed in there. One named "IV_MARK_SURFACE" (Front), and one named "IV_MARK_SURFACE_BACK" (Back). We can also save those export settings configuration out to an 'INI' file, so that we can use it again later. When exporting from a drawing, instead of directly from the model, I'm not sure if we can use the same INI file that we created on the model side, but specifying an INI file is the only option we have when going through the TranslatorAddIn.SaveCopyAs method. If attempting to export directly from the model by code, I think our only option is to use the FlatPattern.DataIO.WriteDataToFile method, which forces us to use a single String type value. That one String must contain all those specifications, which can make it potentially super long, really complexly formatted.
Wesley Crihfield

(Not an Autodesk Employee)