Below is the only information I can find on advanced settings, which really doesn't help much. Any insight would be appreciated.
Setting advanced print options
You can set the properties of the printParams object to specify advanced options including output, marks and bleeds, transparency flattening, PostScript options, and font options.
Specifying output settings
You can obtain a listing of printer color spaces available by invoking the app object printColorProfiles method. You can then assign one of these values to the printParams object colorProfile property.
In addition, you can set the flags property of the printParams object to specify advanced output settings, such as applying proof settings, shown in the example below:
var pp = this.getPrintParams();
var fv = pp.constants.flagValues;
pp.flags |= fv.applySoftProofSettings;
The PrintParams object offers a lot of options, but not all. You need to read it carefully and see if it offers what you need... I couldn't find it, although I did find some references in various properties to printing separations (such as the preserveOverprint flag under rasterFlags).
I couldn't find it anywhere myself. It seems odd that InDesign and Illustrator have access to these parameters but not Acrobat. Maybe it will be added at some point.