I first thought, can we use function copyDefaultConfig here when placing the file? Except, when I updated this last time it also added a couple new entries, which I suppose we would not want to miss out on.

You can't use copyDefaultConfig because the file is updated upstream and updates will not copy when a new version is added.

So could we use sed or something, then, to add the fix automatically? Or, why do we even have to do this manually, why is this just not the default already; is the glitch specific to a certain hardware/platform?

The default is the opposite (copyDepthToRDRAM=1), so it's clearly a platform (RaspberryPi / GLES3) glitch

[DONKEY%20KONG%2064] Good_Name=Donkey Kong 64 (E)(J)(U) frameBufferEmulation\copyDepthToRDRAM=1 frameBufferEmulation\N64DepthCompare=0

The launch script has some overrides for games, but copyDepthToRDRAM is not among the settings considered. Maybe it would be useful to have a GLideN64.local.conf and merge the settings from it in GLideN64.custom.conf, during installation/configuration.

Updating/installing with a down mirror?