If your flatpak is vscodium and you want to run it using code command.
It is not much different than a java app packed as jar ([root tip] [How To] I have downloaded a program as a jar file - what now?)
Ensure the ~/.local/bin folder exist
mkdir -p ~/.local/bin
Create the script (this is a herefile - you could use any editor of choice (copy paste line 2 and 3))
cat << EOF > ~/.local/bin/code
#!/usr/bin/env bash
flatpak run com.vscodium.codium "\$@" &
EOF
Make the script executable
chmod +x ~/.local/bin/code