What kind of issues did/do you encounter?

The VS Code/Codium essentially provide a separate development environment within the flatpak container. All the tools there, and the shell are separate from your actual system. There are some ways to work around this (https://github.com/flathub/com.vscodium.codium/blob/master/README.md). I gave up on the Flatpak and installed a native package. Containers are nice, but they have their limitations.