How can the default save format be changed for OS X Preview app?
Unless you need to edit the image in Preview, I'd suggest leaving it out of the equation altogether.

I use the following python script which saves any image on the clipboard to a PDF file, using a save dialog. (If the file exists, it adds the image as a new page.)
You can embed it in an Automator workflow with a Run Shell Script action, or add it to the /Library/Scripts folder, and you can access it using the Scripts menulet. (Script Editor.app Preferences enable the menulet.)

#!/usr/bin/python

from AppKit import NSPasteboard, NSPasteboardTypePDF, NSPasteboardTypeTIFF, NSPasteboardTypePNG, NSTIFFPboardType, NSPICTPboardType, NSImage, NSSavePanel, NSApp
from Foundation import NSURL
import Quartz as Quartz
import os, syslog

def save_dialog(directory, filename):
    panel = NSSavePanel.savePanel()
    print (panel)
    panel.setTitle_("Save clipboard")
    myUrl = NSURL.fileURLWithPath_isDirectory_(directory, True)
    panel.setDirectoryURL_(myUrl)
    panel.setNameFieldStringValue_(filename)
    NSApp.activateIgnoringOtherApps_(True)
    ret_value = panel.runModal()
    if ret_value:
        return panel.filename()
    else:
        return ''

def main():
    destination = os.path.expanduser("~/Desktop/")
    outfile = save_dialog(destination, "Clipboard.pdf")

    myFavoriteTypes = [NSPasteboardTypePDF, NSPasteboardTypeTIFF, NSPasteboardTypePNG, NSTIFFPboardType, NSPICTPboardType, 'com.adobe.encapsulated-postscript']
    pb = NSPasteboard.generalPasteboard()
    best_type = pb.availableTypeFromArray_(myFavoriteTypes)
    if best_type:
        clipData = pb.dataForType_(best_type)
        if clipData:
            image = NSImage.alloc().initWithPasteboard_(pb)
            if image:
                page = Quartz.PDFPage.alloc().initWithImage_(image)
            if os.path.exists(outfile):
                pdfURL = NSURL.fileURLWithPath_(outfile)
                myFile = Quartz.PDFDocument.alloc().initWithURL_(pdfURL)
                if myFile:
                    pagenum = myFile.pageCount()
                    myFile.insertPage_atIndex_(page, pagenum)
                    print ("Image added to Clipboard file.")

            else:
                pageData = page.dataRepresentation()
                myFile = Quartz.PDFDocument.alloc().initWithData_(pageData)
            myFile.writeToFile_(outfile)
            print ("Clipboard file created.")

    else:
        print ("No clipboard image data was retrieved.")
        print ("These types were available:")
        print (pb.types())

if __name__ == "__main__":
    main()