From your comments, it seems disingenuous to say a good number of emulator devs when it's really only PCSX2 (and I'm not sure where that statement on refusing to cooperate originated from, which is unfortunate to see). Based off the Discord link you shared, I think you accidentally went into the conversation without a lot of key information (which can be found on EmuDeck's wiki and GitHub repo).
EmuDeck downloads the AppImage of PSCX2 not the Flatpak. EmuDeck configures only a few things with PCSX2 (namely the renderer which was recently fixed and should now be removed in the config, file paths, and big picture mode). In addition to those, controls and hotkeys are also configured.
To be synchronous with PSCX2's recommendations, that renderer should be flipped back to auto from vulkan, the big picture flag removed, and the paths to use symlinks instead. Other than those 3 items, there are no real erroneous configurations (that I'm aware of) that should be in disconnect with what PCSX2 wants. These configs shouldn't affect performance at all. I may PR these 3 items sometime soon, but again these don't cause any issues in the games themselves.
The PCSX2 auto-updater you mention being broken works completely fine, I don't know why it doesn't work on your end. Anyway, I'm not sure of any major conflict with other dev teams. And hopefully a PR with the above fixes should get EmuDeck back in good graces with PCSX2.
And to re-affirm, it's really important to go into a support conversation understanding the tools you are using, the Discord conversation linked is sort of a hot mess of misinformation (since PCSX2 likely doesn't use EmuDeck to use their own emulator, the user should know what they're using to best receive support).
From your comments, it seems disingenuous to say a good number of emulator devs when it's really only PCSX2 (and I'm not sure where that statement on refusing to cooperate originated from, which is unfortunate to see). Based off the Discord link you shared, I think you accidentally went into the conversation without a lot of key information (which can be found on EmuDeck's wiki and GitHub repo).
EmuDeck downloads the AppImage of PSCX2 not the Flatpak. EmuDeck configures only a few things with PCSX2 (namely the renderer which was recently fixed and should now be removed in the config, file paths, and big picture mode). In addition to those, controls and hotkeys are also configured.
To be synchronous with PSCX2's recommendations, that renderer should be flipped back to auto from vulkan, the big picture flag removed, and the paths to use symlinks instead. Other than those 3 items, there are no real erroneous configurations (that I'm aware of) that should be in disconnect with what PCSX2 wants. These configs shouldn't affect performance at all. I may PR these 3 items sometime soon, but again these don't cause any issues in the games themselves.
The PCSX2 auto-updater you mention being broken works completely fine, I don't know why it doesn't work on your end. Anyway, I'm not sure of any major conflict with other dev teams. And hopefully a PR with the above fixes should get EmuDeck back in good graces with PCSX2.
And to re-affirm, it's really important to go into a support conversation understanding the tools you are using, the Discord conversation linked is sort of a hot mess of misinformation (since PCSX2 likely doesn't use EmuDeck to use their own emulator, the user should know what they're using to best receive support).