global custom_viewport_xxx settings not preserved when saving configuration

Description

Custom Viewport settings are replaced when saving overrides.

if i have something like this in my global retroarch.cfg

custom_viewport_height = "720"
custom_viewport_width = "960"
custom_viewport_x = "480"
custom_viewport_y = "180"

i expect them to not be touched when i both save core override or configuration.

Expected behavior

I tested it in fuse and snes9x. i expect i.e. when choosing 'save core override' for fuse, that it creates a fuse.cfg with just the options i change.

in my particular case, i have runahead settings enabled in the global configuration.
since it seems to break fuse i want to disable them just for it. so, i expect the following core override file is being generated when i disable the runahead option in fuse:

[fuse.cfg]
run_ahead_enabled = "false"

Actual behavior

without me touching anything about scaling settings, the following fuse.cfg is created instead

[fuse.cfg]
custom_viewport_height = "960"
custom_viewport_width = "1280"
custom_viewport_x = "320"
custom_viewport_y = "60"
run_ahead_enabled = "false"

Steps to reproduce the bug

1. have a global retroarch.cfg with some custom scaling settings set as above, and runahead enabled.
2. go in fuse, or snes9x (but indeed i suspect this is a retroarch bug), disable runahead settings
3. save core override (or current configuration)
4. check the generated file

Version/Commit

RetroArch: 1.8.5 8bcd74b

Environment information

Raspberry PI 4 / Retropie

Start by reproducing the save-core-override steps with global custom viewport settings and runahead enabled, then trace the configuration-saving entry point that generates the override file. Done means saving the override preserves the global viewport values and writes only the changed runahead setting, as shown in the issue.