http://standards.freedesktop.org/basedir-spec/basedir-spec-latest.html
XDG Base Directory Specification requires $HOME/.config/ppsspp should be used

$XDG_CONFIG_HOME defines the base directory relative to which user specific configuration files should be stored. If $XDG_CONFIG_HOME is either not set or empty, a default equal to $HOME/.config should be used.

please use $HOME/.config/ppsspp for both Qt and SDL version.

or separately:
$HOME/.config/ppssppqt for Qt settings
$HOME/.config/ppsspp for ppsspp

thanks

thanks.