I don't know if OpenAsar is exactly overriding them but when OpenAsar installed there's no title bar under GNOME Wayland. Electron apps needs to have --enable-features=WaylandWindowDecorations to have title bar working under GNOME Wayland environment. Because of this, the flatpak build of Discord uses a startup script that passes those required parameters to the Discord process. It looks like, a parameter that only exists in flatpak script still works, but if the parameter exists in both flatpak script and OpenAsar (--enable-features in this case) the flatpak parameters are getting overridden by OpenAsar.
https://github.com/GooseMod/OpenAsar/blob/main/src/cmdSwitches.js
https://github.com/flathub/com.discordapp.Discord/blob/master/discord.sh#L9
I don't know if OpenAsar is exactly overriding them but when OpenAsar installed there's no title bar under GNOME Wayland. Electron apps needs to have --enable-features=WaylandWindowDecorations to have title bar working under GNOME Wayland environment. Because of this, the flatpak build of Discord uses a startup script that passes those required parameters to the Discord process. It looks like, a parameter that only exists in flatpak script still works, but if the parameter exists in both flatpak script and OpenAsar (--enable-features in this case) the flatpak parameters are getting overridden by OpenAsar.
https://github.com/GooseMod/OpenAsar/blob/main/src/cmdSwitches.js
https://github.com/flathub/com.discordapp.Discord/blob/master/discord.sh#L9