How to make default background ALWAYS transparent

Do you need an empty bottom layer?

The preset for the clipboard is dynamically created for the size of the Image that is currently in the clipboard and generated will be a preset with a background layer that is white. If the Clipboard is empty you will not see a new document preset for a clipboard size document.

Now I do a lot of screen captures and stack them then expand the canvas and position layers over the expanded canvas area. I do not mind if there is a white background layer I can always tun its visibility off or delete the layer it not required.

I do some many screen captures  I have  automated the process all I need to  do is tap a function key that will play an action that will run my append clipboard  script.  The Script will switch to my Clipboard document paste in the clipboard.  Find the Size of the new layer expand the canvas to house a layer that size and position the layer over it.  If my Clipboard document does not exist the script will create it and paste in the clipboard and adjust the canvas size for the layer.  The Clipboard document created could be crated with a transparent layer If I needed it.   I can not remember how I created it for the layers created background or transparent is not needed so after the script adjust canvas size for the pasted in layer the script delete the layer the Document was created with. My Clipboard document has no background layer. The bottom layer is the first pasted in clipboard contents.

/* ==========================================================
// 2013  John J. McAssey (JJMack) 
// ======================================================= */
// This script is supplied as is. It is provided as freeware. 
// The author accepts no liability for any problems arising from its use.

// I set a shortcut key in my case F5 to this Photoshop script mainly for doing Window screen capturing of:
// desktop displays, Active window and selected area copy to clipboard. The script log the cardboard into a document with the name clipboard. 

/*
<javascriptresource>
<about>$$$/JavaScripts/AppendClipboard/About=JJMack's Append Clipboard into Clipboard document.^r^rCopyright 2014 Mouseprints.^r^rJJMack's Script.^r
NOTE:New Clipboard Document will be open if necessary</about>
<category>JJMack's Script</category>
</javascriptresource>
*/

// enable double-clicking from Mac Finder or Windows Explorer
#target photoshop // this command only works in Photoshop CS2 and higher

// bring application forward for double-click events
app.bringToFront();

if (!documents.length) {
	NewCliboardDoc (); 
	app.activeDocument.suspendHistory('appendClipboard','main(true)'); // New document opened proceed
	}
else { 	//locate Document clipboard
	for (var i=0;i<app.documents.length;i++) { 
		app.activeDocument=app.documents[i];
		if (app.activeDocument.name == "Clipboard"){break;}
		}
	if (app.activeDocument.name != "Clipboard"){
		NewCliboardDoc ();
		app.activeDocument.suspendHistory('appendClipboard','main(true)'); // New document opened proceed
		}
	else {app.activeDocument.suspendHistory('appendClipboard','main(false)'); }	// Old Clipboard Document found
	}

///////////////////////////////////////////////////////////////////////////////
//                            main function                                  //
///////////////////////////////////////////////////////////////////////////////
function main(newFile) {
	// declare local variables
	var orig_ruler_units = app.preferences.rulerUnits;
	app.preferences.rulerUnits = Units.PIXELS;			// Set the ruler units to PIXELS

	try { 
		activeDocument.paste(); 					    // past in clipboard may fail enclose in try
		var LB = app.activeDocument.activeLayer.bounds;	// Get the bounds of the work layer
		var LWidth = (LB[2].value) - (LB[0].value);		// Area width
		var LHeight = (LB[3].value) - (LB[1].value);	// Area height
		// BOTTOMCENTER BOTTOMLEFT BOTTOMRIGHT MIDDLECENTER MIDDLELEFT MIDDLERIGHT TOPCENTER TOPLEFT TOPRIGHT
		if(newFile) {
			app.activeDocument.resizeCanvas(LWidth, LHeight, AnchorPosition.TOPLEFT);
			app.activeDocument.layers[1].remove();
			}
		else {
			if (LWidth>=app.activeDocument.width) {	app.activeDocument.resizeCanvas(LWidth, app.activeDocument.height + LHeight, AnchorPosition.TOPLEFT);}
			else {app.activeDocument.resizeCanvas(app.activeDocument.width, app.activeDocument.height + LHeight, AnchorPosition.TOPLEFT);}
			}
		app.activeDocument.selection.selectAll();		// select all
		// Left('AdLf'); Right('AdRg'); Top('AdTp'); Bottom('AdBt'); Center Horizontal('AdCH'); Center Vertical('AdCV');
		align("AdLf");align("AdBt");					//Align to selection Left bottom
		app.activeDocument.selection.deselect();
		SetViewFitonScreen();
		//app.purge(PurgeTarget.CLIPBOARDCACHE);
		}
	catch(e) { 
		if(newFile) app.activeDocument.close(SaveOptions.DONOTSAVECHANGES);
		alert("Clipboard Empty"); 
		}		

	app.preferences.rulerUnits = orig_ruler_units;			// Reset units to original settings
	}
///////////////////////////////////////////////////////////////////////////////
//                           main function end                               //
///////////////////////////////////////////////////////////////////////////////
function NewCliboardDoc () {
	// app.documents.add([width][, height][, resolution][, name][, mode][, initialFill][, pixelAspectRatio][, bitsPerChannel][, colorProfileName])
	var Clipboard = app.documents.add( null, null, 100, "Clipboard", NewDocumentMode.RGB, null, null, null, "sRGB IEC61966-2.1");
	}

function align(method) {
	var desc = new ActionDescriptor();
			var ref = new ActionReference();
			ref.putEnumerated( charIDToTypeID( "Lyr " ), charIDToTypeID( "Ordn" ), charIDToTypeID( "Trgt" ) );
		desc.putReference( charIDToTypeID( "null" ), ref );
		desc.putEnumerated( charIDToTypeID( "Usng" ), charIDToTypeID( "ADSt" ), charIDToTypeID( method ) );
	executeAction( charIDToTypeID( "Algn" ), desc, DialogModes.NO );
	};

function SetViewFitonScreen() {
    var desc1 = new ActionDescriptor();
    var ref1 = new ActionReference();
    ref1.putEnumerated(charIDToTypeID('Mn  '), charIDToTypeID('MnIt'), charIDToTypeID('FtOn'));
    desc1.putReference(charIDToTypeID('null'), ref1);
    executeAction(charIDToTypeID('slct'), desc1, DialogModes.NO);
};

The default is for new documents to have a background layer. You can't change that. You could try setting a script or action to run on new document creation.

https://helpx.adobe.com/photoshop/user-guide.html?topic=/photoshop/morehelp/automation.ug.js