I found a way to do this for flatpak applications.
Create a bash script that calls the editor and passes the file to be opened as a parameter. Save those scripts and call them as external editor in Bootstrap Studio.
It took a bit of searching to find the right parameters. I use Linux Mint 22.1 Cinnamon and was able to use the program launcher command from the menu as a basis. Instead of %F, I had to use $@.
See my two bash scripts below.
bash script notepad-next.sh:
#!/bin/bash
/usr/bin/flatpak run --branch=stable --arch=x86_64 --command=NotepadNext --file-forwarding com.github.dail8859.NotepadNext @@ $@ @@
bash script visual-studio-code.sh:
#!/bin/bash
/usr/bin/flatpak run --branch=stable --arch=x86_64 --command=code --file-forwarding com.visualstudio.code --reuse-window @@ $@ @@