IMO current assumption that .jpg files should be used is a wrong one, as a jpg doesn’t support transparency and mouth need transparency . So my suggestion is either make code that will make possible for user to change format for papagayo import or set format to png.
You just need to write ‘PNG’ on the third row of the 'lst file your exported file from Papagayo and you’re done.
But yes, better have PNG by default. Welcome to the Synfig issues tracker