Hi,
inside .bashrc
you can check if the file is executed inside a toolbox environment. Maybe that helps you at least a bit.
if ! [ -f /run/.containerenv ] \
|| ! [ -f /run/.toolboxenv ]; then
# not executed inside toolbox
alias emacs="flatpak run org.gnu.emacs"
alias vim="flatpak run org.vim.Vim"
alias mutt="toolbox run -c mailbox-2 mutt"
fi
If you dont want to share your home dir with the toolbox you should think about building a container from scratch using podman.