I don't know why you couldn't create a config file to run your console application, .

I have done this:

• (/bin/bash in terminal, libertine container)

fakeroot apt update
fakeroot apt install sway

• use OpenStore tedit text editor app to write the desktop entry,

Version=1.0
Type=Application
Terminal=false
Exec=libertine-launch -i [container name] sway
Name=Sway app window manager, i3 compatible WM
X-Lomiri-Touch=true
X-Lomiri-Default-Department-ID=accessories
X-Ubuntu-Touch=true
X-Ubuntu-Default-Department-ID=accessories

• then

cp -v ~/.local/share/tedit.danfro/libertine-application-container-sway.desktop.txt ~/.local/share/applications/libertine-application-container-sway.desktop