Batch image trace with transparent background

@Red_Point, How do you share these custom settings with other users? I find it rather cumbersome to share custom "Trace" settings since it requires updating an "Preference" file buried in a Preference folder that is not well document (at least in older AI CC versions).

I also find it combursome to rely on a 2nd application for a routine Illustrator function such as "Trace". 

Yes, you can create a custom Image Trace preset, but at least in AI CC 2015 an Action will always use the default trace settings.

To get around this we edited the "Tracing Presets" file so the "Default" preset produces a transparent background (Black and White only).

This file is found in various locations depending on your system and AI version. Check this thread for help finding it:
How to share custom Image Trace Presets between users?

You can edit the "Vectorizing Presets" file in a text editor to get the "Default" Setting you need. Alternatively you could write a script to use ANY named preset and use the script in your batch operation. This is the JavaScript we use for this purpose. You might use a portion of it for your needs:

function traceFPrint(PIN) {
    // Trace PNG to Vector in Illustrator
    var aDoc = app.activeDocument;
    var Selected = aDoc.selection[0]
    var Tracing_Preset = '[Default]';
    var sel = aDoc.selection;
    var f = 15; //percent of current size  
    var pItems = aDoc.pageItems;
    //Scale Fingerprint  Image
    for (var i = 0; i < pItems.length; i++) {
        pItems[i].resize(f, f, true, true, true, true, f, Transformation.DOCUMENTORIGIN);
    };
    fitArtboards(app.activeDocument);
    // Trace Fingerprint  
    for (var i = 0; i < sel.length; i++) {
        if (sel[i] == '[RasterItem ]') {
            var pic = sel[i].trace();
            pic.tracing.tracingOptions.loadFromPreset(Tracing_Preset);
            pic.tracing.expandTracing().selected = true;
        }
    }
    aDoc.layers[0].groupItems[0].name = PIN;
    zoomToSelection ();
    aDoc.activeLayer.hasSelectedArtwork = false;
}