You can rpm-ostree layer any Fedora package - there’s no special “rpm-ostree package”. That being said, installing node.js and npm on the host won’t do you much good, since your IDE will have no more access to host environment than it does to the environment inside a toolbox.It will only see what’s available in the Flatpak sandbox.
Options you have:
- Install the IDE in your home directory, and run it from within the toolbox environment. You’ll have to launch it from the command line or add your own desktop file within ~/.local/share/applications.
- Install the org.freedesktop.Sdk.Extension.node10 Flatpak SDK extension. As long as you just need NPM and the IDE, this works fine, but your development environment will have no access to Fedora packages or utilities.
Bridging between a Flatpak installed IDE and a Toolbox only really works for GNOME Builder or Visual Studio Code at the moment.