Incompatibility of anything by merely installing sandbox-app-launcher without using it seems very unlikely at this point. All that sandbox-app-launcher package does is a few dependencies (at time of writing sudo, bubblewrap, apparmor, libseccomp-dev, helper-scripts, dbus-x11) which by itself don’t do anything. Just extra files on the disk which remain dormant unless used by starting these / configuration of these. sandbox-app-launcher is essentially a wrapper around bubblewrap.
Yes. Ideally we could start a flatpak application through sandbox-app-launcher. I.e.
sandbox-app-launcher flatpak run org.org.Applicationname
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No, the sandbox isn’t optional. You can only poke holes in it.