Settings removed from user's retroarch.cfg are autofilled with wrong defaults

When the user individually removes a setting from the user's retroarch.cfg, RetroArch automatically fills the config file with defaults that appear to be standard Linux ones, rather than those provided by the system retroarch.cfg included by the Flatpak installation. This is in opposition to a complete removal of user's config, in which case the system retroarch.cfg is correctly taken into account when generating a new .cfg.
For instance: in the Flatpak build, retroarch.cfg created from scratch includes video_record_quality = "6", as per the system retroarch.cfg, but if video_record_quality = "6" is wiped from user's cfg., then RetroArch launched and closed, video_record_quality = "2" is added to user's retroarch.cfg instead.

Begin by reproducing the two configuration-removal paths in the Flatpak build: create retroarch.cfg from scratch, then delete video_record_quality from an existing user config and relaunch RetroArch. Compare the resulting values with the system retroarch.cfg; done means both paths use the expected system-provided default.

Written by the indexing model from the issue text.