For a pdf to have transparent background with MuPDF go to the C program file("mupdf.c") remove the code that sets the background to white and replace it with fz_clear_pixmap(ctx, pix);
ie, replace fz_clear_pixmap_with_value(ctx, pix, 0xff);
with fz_clear_pixmap(ctx, pix);
after editing rebuild the ndk, and use it in your android app.