You can, and should do that. Here’s what that looks like: toolbox run -c <toolbox-name> <command>

All of my development tools are in a toolbox, including my IDE (Sublime Text). I created a standard .desktop file so that I can launch it like any other application, and it works perfectly, with a proper Icon and everything. Example:

[Desktop Entry]
Version=1.0
Type=Application
Name=Sublime Text
GenericName=Text Editor
Comment=Sophisticated text editor for code, markup and prose
Exec=/usr/bin/toolbox run -c devel /opt/sublime_text/sublime_text %F
Terminal=false
MimeType=text/plain;
Icon=/home/user/.local/share/applications/SublimeText.png
Categories=TextEditor;Development;
StartupNotify=true
StartupWMClass=sublime_text

To run something on the host from inside a toolbox, you can use flatpak-spawn:

$ toolbox enter ...
$ flatpak-spawn --host <command> <args>

You can even use that to (awkwardly) run something in another toolbox using the same command above:

flatpak-spawn --host toolbox run -c <other-container> <command>

Sublime text specifically has support for custom build commands. Sometimes, I’m using it to develop something in a different toolbox than the one sublime is installed in. So in my custom build script for the project, I add a check to enter the correct toolbox before executing the build. Here’s what that looks like:

TARGET_TOOLBOX=example
source /run/.containerenv
if [ "$name" != "${TARGET_TOOLBOX}" ]; then
	echo "SWITCHING CONTAINER $0 $@";
	flatpak-spawn --host toolbox run --container ${TARGET_TOOLBOX} /usr/bin/env zsh -c "$0 $@";
	exit 0;
fi

#proceed with build...

This container/toolbox workflow is far superior to anything else, as it makes it trivial to quickly test whether your code works on a different distros/versions. It all just works with your existing tooling/local workflows once you learn how to work with the tools. There really is nothing you can’t do.

…and that’s for development, which is the most difficult scenario for this type of thing. For regular every day users, immutability just works without requiring people to learn anything new besides reaching for flatpak instead of apt/dnf/pacman/etc.