When I try to edit the Shift + F9 item in the cfg file with a desired screen resolution & refresh rate it simply gets overwritten back to its default value on game launch.

Over at Options > Screens I have limited resolutions and refresh rate choices (doesn't match what I see in windows advanced display settings).

Anyone have any ideas if there is a way to manually override this?

Hello. As far as I understand it how it ussually goes there is a check about what display settings are supported. Its either that you have the game display connected to a adapter that reports a limited ammount of settings or you might not have a driver or not have a correct driver installed.
Also I dont think there is an override but a solution could be Shift+F4 and maximize the window.
I belive Ctrl+C is "clip mouse to window" so your mouse does not exit the window.

try setting the cfg file to read-only?

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try setting the cfg file to read-only?

Setting it to read-only prevents the cfg file from being overwritten but the game still defaults to original resolution of 1920 X 1048 60hz.

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I don't think there is an override but a solution could be Shift+F4 and maximize the window.

This works but the refresh rate stays locked at 60Hz instead of 120 which windows is running at.

Turns out it is an issue with my monitor. Older BENQ models have higher refresh rates such as 120 and 144 restricted to DVI-D cables only while HDMI & Display Port stays locked at 60Hz.

So I'm just going to use my laptop's display for now.

You could try to create a custom resolution with Custom Resolution Utility 1.5.2.
And the resolution/refresh rate you add with this program - it will be visible in LFS too.