Issues with Custom Options about cheatdeck HOT 3 OPEN

Also, deleting the custom option doesn't appear to remove the option from launch options. I have to manually go to launch options and remove it.

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The modified options with a new field would be a "new" options, so the changes from custom list (local storage) will never affect the launcher options, unless you explicitly toggle and save it, because some other apps like EmuDeck and Heroic launcher make their own launch options.
The new value seems to be never applied is a bug, I didn't check the value change, glad you pointed it out, it should be fixed now. A modified value will be show as a disabled option.
I am not sure if there are any better ways to do it or suggestions, so I will keep this issue open

from cheatdeck.

The custom options items are stored at local storage, they are not for only the current game, you can quick access them in any other games, so the change of the custom items will never affect the current games launch options

from cheatdeck.