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I don't know anything about Flatpak, it's not related to PPSSPP project in any way and PPSSPP release there is in no way official, however font override path is "memorystick:/PSP/flash0/font/" - so you might try that as long as you do have access to memory stick.
http://forums.ppsspp.org/showthread.php?tid=6594 - Custom PPSSPP Shaders!
http://forums.ppsspp.org/showthread.php?tid=3590&pid=117172#pid117172 - simple CE scripts to help creating CWCheats,
https://github.com/LunaMoo/PPSSPP_workarounds - CWCheat workarounds.