BTW as for Atom I’ve created some wrapper scripts for things I use and that needs to be spawned on the host system.
Actually, I guess, you can use the exact same ones for VS Code/OSS Code (see difference here), too. Or any other IDE in a flatpak, for that matter.
It is based on the suggestion by @refi64 to use flatpak-spawn. Explanation on how to setup it is there in the repo.