

Not quite, but this did lead me to my answer, thank you.
Very confusingly, EmulationStation and ES-DE are more distinct now than you might suspect, this is a problem I keep running up against. I found my answer in the ES-DE documentation for Steam Deck/SteamOS, https://emudeck.github.io/tools/steamos/es-de/#es-de-folder-locations (note that EmulationStation uses .cfg in the format of XML I guess whereas ES-DE uses .xml files directly)
The solution was to take my currently working /usr/share/es-de/resources/systems/linux/es_systems.xml file and copy it to ~/ES-DE/custom_systems and now it looks like the AppImage has fully picked up all my systems and configurations from the AUR install so I can safely switch over. I’d still like to resolve the AUR issues, but we’ll treat that separately, I’m just happy to have a working solution right now 😊
Yeah, sometimes I’m just standing in the shower in the morning planning out my day and I think to myself, “I should attack Ukraine.” /s