If you want to specify the location of custom fonts using the pdf-fontsdir attribute, yet still be able to reference the bundled fonts, you need to refer to the bundled fonts using the GEM_FONTS_DIR token. To do so, you can either a) prefix the path of the bundled font in the theme file with the segment GEM_FONTS_DIR (e.g., GEM_FONTS_DIR/mplus1p-regular-fallback.ttf, or b) use relative paths in the theme file and include GEM_FONT_DIR in the value of the pdf-fontsdir attribute separated by the location of your custom fonts using a comma (e.g., path/to/your/fonts,GEM_FONTS_DIR) or a semi-colon (e.g., path/to/your/fonts;GEM_FONTS_DIR).