I still need to worry about permission. Other apps CANNOT access the root folder of PerAppFonts. /assets/fonts can only be used when compiling which defeats the purpose. (you have to compile and recompile for every single font.
The current problem is NOT permissions now. It is the directory that the fonts are being stored. /sdcard/ , /mnt/sdcard/ and /storage/sdcard/ are the directories that is usable by the system in the boot process. However, due to multi-user capabilities in Android 4.2+, Android has /storage/emulated/<UserNumber>/ which is initialized after PerAppFonts attempts to find the fonts.