Emudeck is heavily discouraged and unsupportorted by a good number of emulator dev teams for refusing to cooperate with them. Emudeck builds configuration files for you, not shying away from not recommended settings and causing issues in some emulators and games.
Also, some emulators have their source code edited and the changes are not documented/not public.
Unfortunately I don't have an external link about it, can only pin point a quite lenghty conversation and support request I had with a couple of the PCSX2 developers that happened in their Discord server. You can jump to the start of the conversation (if you are in the PCSX2 Discord server) using this link.
The conversation started after I asked them for support for the render window not taking the whole screen when attached to a 4:3 monitor, and told me about why they don't support at all PCSX2 installs made my Emudeck. Duckstation appears to also not support Emudeck for the lack of cooperation from the project.